FunRegions - Spatial Region Filtering
This document contains a summary of the user interface for spatial region filtering images and tables.
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.
Spatial region filtering for images and tables is accomplished by means of region specifications. A region specification consists of one or more region expressions, which are geometric shapes,combined according to the rules of boolean algebra. Region specifications also can contain comments and local/global processing directives.
Typically, region specifications are specified using bracket notation appended to the filename of the data being processed:
It is also possible to put region specification inside a file and then pass the filename in bracket notation:
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 API to open filters explicitly.
More specifically, region specifications consist of one or more lines containing:
# 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], ...
A single region expression consists of:
# parens and commas are optional, as is the + sign [+-]shape(num , num , ...) OP1 shape num num num OP2 shape ...
([+-]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
Thus, a region descriptor consists of one or more region expressions or regions, separated by comas, new-lines, or semi-colons. Each region consists of one or more geometric shapes combined using standard boolean operation. Several types of shapes are supported, including:
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
In addition, the following regions accept accelerator syntax:
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
Note that the circle accelerators are simply aliases for the annulus accelerators. See region geometry for more information about accelerators.
Finally, the following are combinations of pie with different shapes (called "panda" for "Pie AND Annulus") allow for easy specification of radial sections:
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
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.
The following "shapes" are ignored by funtools (generated by ds9):
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
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 WCS header, that angle is added implicitly as well.
Note that 3-letter abbreviations are supported for all shapes, so that you can specify "circle" or "cir".
Columns Used in Region Filtering
By default, the x,y values in a region expression refer to the two "image binning" 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.
Alternate columns for region filtering can be specified by the syntax:
(X,Y)=annulus(x,y,ri,ro) (PHA,PI)=circle(x,y,r) (DX,DY)=ellipse(x,y,a,b[,angle])
(See also Region Algebra for more complete information.)
Region shapes can be combined together using Boolean operators:
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
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,
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 field(), as in:
field() && !circle(512,512,10)
Region Separators Also Are Operators
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 OR operator is automatically generated in its place but, unlike explicit use of the OR operator, the region ID is incremented (starting from 1).
For example, the two shapes specified in this example are given the same region value:
On the other hand, the two shapes defined in the following example are given different region values:
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 OR 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.
In general, commas are used to separate region expressions entered in bracket notation on the command line:
# regions are added to the filename in bracket notation foo.fits[circle(512,512,100),circle(400,400,20)]
New-lines are used to separate region expressions in a file:
# 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)
Semi-colons are provided for backward compatibility with the original IRAF/PROS implementation and can be used in either case.
If a pixel is covered by two different regions expressions, it is given the mask value of the first region that contains that pixel. That is, successive regions do not overwrite previous regions in the mask, as was the case with the original PROS 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 before M, or else it will be "covered up" by the latter.
Shapes also can be globally excluded from all the region specifiers in a region descriptor by using a minus sign before a region:
operator arguments: -------- ----------- - Globally exclude the region expression following '-' sign from ALL regions specified in this file
The global exclude region can be used by itself; in such a case, field() is implied.
A global exclude differs from the local exclude (i.e. a shape prefixed by the logical not "!" 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.
The @filename directive specifies an include file containing region expressions. This file is processed as part of the overall region descriptor:
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 "pi==1" and foo2 contains "pha==2" then the following expressions are equivalent:
"[@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]"
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:
circle 512 512 10 circle 520 520 10
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:
since this is equivalent to:
pi==4 && (circle 512 512 10 ⎪⎪ circle 520 520 10)
If you leave out the parenthesis, you are filtering this statement:
pi==4 && circle 512 512 10 ⎪⎪ circle 520 520 10)
which is equivalent to:
(pi==4 && circle 512 512 10) ⎪⎪ circle 520 520 10)
The latter syntax only applies the pi test to the first region.
For image-style filtering, the @filename can specify an 8-bit or 16-bit FITS 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.)
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 FITS 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.
Global and Local Properties of Regions
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 global keyword specifies properties and qualifiers for all regions, while local properties are specified in comments on the same line as the region:
global color=red circle(10,10,2) circle(20,20,3) # color=blue circle(30,30,4)
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.
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:
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
Specifying Positions, Sizes, and Angles
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:
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
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
When a "pure number" (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:
All pure numbers have implied units corresponding to the current coordinate system.
If no such system is explicitly specified, the default system is implicitly assumed to be PHYSICAL.
In practice this means that for IMAGE and PHYSICAL systems, pure numbers are pixels. Otherwise, for all systems other than linear, pure numbers are degrees. For LINEAR systems, pure numbers are in the units of the linear system. This rule covers both positions and sizes.
The input values to each shape can be specified in several coordinate systems including:
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
If no coordinate system is specified, PHYSICAL is assumed. PHYSICAL 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.,
global coordsys physical circle 6500 9320 200
The use of celestial input units automatically implies WORLD coordinates of the reference image. Thus, if the world coordinate system of the reference image is J2000, then
circle 10:10:0 20:22:0 3'
is equivalent to:
circle 10:10:0 20:22:0 3' # j2000
Note that by using units as described above, you may mix coordinate systems within a region specifier; e.g.,
circle 6500 9320 3' # physical
Note that, for regions which accept a rotation angle:
ellipse (x, y, r1, r2, angle) box(x, y, w, h, angle)
the angle is relative to the specified coordinate system. In particular, if the region is specified in WCS coordinates, the angle is related to the WCS system, not x/y image coordinate axis. For WCS 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 CROTA value in the WCS parameters) and for these images, the angle will be relative to the WCS axes. In such case, a region specification such as:
fk4;ellipse(22:59:43.985, +58:45:26.92,320", 160", 30)
will not, in general, be the same region specified as:
physical;ellipse(465, 578, 40, 20, 30)
even when positions and sizes match. The angle is relative to WCS axes in the first case, and relative to physical x,y axes in the second.
More detailed descriptions are available for: Region Geometry, Region Algebra, Region Coordinates, and Region Boundaries.
See funtools(7) for a list of Funtools help pages
|April 14, 2011||version 1.4.5|