### Analysis

> Each file type known to DS9 can have user-defined analysis commands associated with it. These analysis commands are defined at start-up time , or loaded by the user, by means of an ASCII analysis description file. The analysis commands are available for execution, either via the Analysis Menu or the XPA point Analysis. In addition, commands may be bound to events, such as keystrokes or mouse clicks. This type of command is called a bind command.

> DS9 searches for an analysis file named `ds9.ans` or `ds9.analysis` in the current directory and `$HOME` to be loaded at startup. In addition, DS9 will search the following directories for any analysis files to be loaded at startup in the form of `*.ds9`: the current directory, `$HOME/bin`, `/usr/local/bin`, `/opt/local/bin`, and `/soft/saord/bin`. Finally, the user may specify analysis files to be loaded at startup in the preferences analysis panel. The user may also load or clear current analysis commands via command line options or the Analysis menu.

> When activated, either from the menu, XPA, or bound event, an analysis command first is macro-expanded to fill in user-defined arguments and then is executed externally. Results may be displayed in a separate text window, plot window, or in a image frame.

> Syntax
> Command Type
> Macros
> Help
> Parameters
> Hierarchical Menus
> Sample

> Syntax

> The analysis file that defines the known analysis commands consists of one or more file descriptors, each of which has the following format:

> > `Menu label to be used`
> > `A space separated list of file templates`
> > `Command type [menu | bind <event>]`
> > `The command line for the analysis program`

> Task names may contain space characters. All lines may be indented. Also, the '#' character is a comment character. A separator can be inserted in the menu by specifying the following sequence '---'.

> `Example:`

> > `# this will insert a menu separator`
> > `---`

> Command Type

> The third line indicates the type of command.

> > menu

> > A `menu` command creates an menu option under the Analysis menu option, and can be invoked by the user via the GUI or XPA.

> > `Example:`

> > > `# Menu command example`
> > > `My Analysis Task`
> > > `` `*.fits`
> > > `menu`
> > > `$data | doit | $text`

> > bind

> > A `bind` command is a command that is bound to an event. When the event occurs, the command is executed. Types of events available include all TK events, including all keystrokes and mouse clicks. If a command is bound to an event other that a keystroke, care must be taken to not to interfere with other internal DS9 events.

> > To bind to a key stroke, use the following command type:

> > > `bind <keystroke>`

> > `Example:`

> > > `# Bind command example`
> > > `Print coordinates`
> > > `*.fits`
> > > `bind x`
> > > `echo "$x $y" | $text`

> > web

> > A `web` command allows the user to invoke the internal web browser from the analysis menu.

> > `Example:`

> > > `# web command example
> > > HTTP based
> > > *
> > > web
> > > http://hea-www.harvard.edu/RD/ds9/ref/index.html
> > > File based
> > > *
> > > web
> > > file:/home/joye/index.html
> > > `

> Macros

> The following macros are macro-expanded to fill in user-defined arguments before the command is executed. Strings that contain $<macroname> that user does not want to be expanded may be escaped by using $$<macroname>. All strings that contain $<string> that are not a macro name will not be affected.

> For example:

> > `echo "$$data $foo" | $text`

> will display a text dialog that contains "$data $foo"

> $width
> $height
> $depth

> Substitute the width, height, or depth of the data file in the command line.

> `Syntax:
> ` `$width`
> `$height`
> `Example:
> ` `echo "$width $height $depth" | $text`

> $bitpix

> Substitute the bitpix of the data file in the command line.

> `Syntax:
> ` `$bitpix`
> `Example:
> ` `echo "$bitpix" | $text`

> $data

> Data from the current frame becomes the input data to the command string. This data is in the form of a FITS image. This macro can only used at the beginning of the command string.

> `Syntax:
> ` `$data`
> `Example:
> ` `$data | dosomething | $text`

> $entry

> Display an entry modal dialog. The returned string is substituted. If `cancel` is selected, the command line is not executed.

> `Syntax:
> ` `$entry(<message>)`
> `Example:
> ` `echo "$entry(Enter something here)" | $text`

> $env

> Substitute the value of a shell environment variable.

> `Syntax:
> ` `$env(<shell variable>)`
> `Example:
> ` `echo "$env(PATH)" | $text`

> $filedialog

> Display the standard file dialog. Substitutes the returned pathname. Argument specifies if an open file or save file dialog is invoked.

> `Syntax:
> ` `$filedialog([open|save])`
> `Example:
> ` `echo "$filedialog(open)" | $text`

> $filename

> Substitute the filename of the data file in the command line. A full filename includes any absolute or relative path. A root filename contains no path. A (2D) subsection defines a subimage from `xmin,ymin` to `xmax,ymax`. For Frame3D, a 2D subsection will also include the current slice (PLANE=) parameter if not 1. A 3D subsection defines a subimage from `xmin,ymin,zmin` to `xmax,ymax,zmax` and no PLANE parameter.

> `Syntax:
> ` `$filename # filename with extname, (2d) subsections, filters`
> `$filename(root|root,base) # root filename with` `with extname,` `no subsections, no filters)`
> `$filename(full|full,base) # full filename` `with extname,` `no subsections, no filters)`
> `$filename(root,3d) # root filename` `with extname,` `3d subsections, filters)`
> `$filename(full,3d) # full filename` `with extname,` `3d subsections, filters)`
> `Example:
> ` `dosomething $filename | $text`
> `dosomething $filename(root) | $text
> ` `dosomething $filename(full,3d) | $text`

> $filename[$regions]

> Combination of `$filename` and `$regions` macros. Generates a series of filenames, each with a region.

> `Syntax:
> ` `$filename[$regions]`
> `$filename[$regions(<options>)]`
> `Example:
> ` `dosomething $filename[$regions] | $text`

> $geturl

> This macro differs from all other macros, including $`url`, in that no subprocess pipe is created. Only HTTP is supported. The contents of the url are retrieved and sent to $`text`, $`plot`, or $`image.` No other processing is allowed. The primary purpose of this macro is to support external analysis for the Windows platform, which has no subprocess support.

> `Syntax:
> ` `$geturl(http://<hostname>:<port>/<query>)`
> `Example:
> ` `$geturl(http://foo.bar.edu/foo.html) | $text`

> $image

> The resulting image data is display in a DS9 frame. This macro should be the last macro of a command line. Optional parameter indicates if a new frame and what type of frame is created for the new data. The macro is removed from the command line before execution.

> `Syntax:
> ` `$image`
> `$image([new|rgb|3d|current])`
> `Example:
> ` `doit | $image(new)`

> $message

> Display a message dialog box, with option buttons. After displaying the message, the macro is removed from the command line before execution. If `cancel` or `no` is selected, the command line is not executed.

> `Syntax:
> ` `$message(<message>)`
> `$message([ok|okcancel|yesno],<message>)`
> `Example:
> ` `$message(okcancel,This is a Message)| doit | $text`

> $null

> Expect no output or results from analysis task. Note: no error message will be returned if the analysis task fails to execute correctly.

> `Syntax:
> ` `$null`
> `Example:
> ` `echo "Hello, world" > foo | $null`

> $pan

> Substitute current pan location of the particular data file are returned. The default coordinate system is `physical`.

> `Syntax:
> ` `$pan
> ` `$pan(<coordinate system>,<format>)`

> where:

> `coordinate system = [image|physical|detector|amplifier|wcs|wcsa...wcsz]`
> `sky frame = [fk4|fk5|icrs|galactic|ecliptic]`
> `sky format = [hms|sexagesimal|degrees]`
> `Example:
> ` `echo $pan(fk5,sexagesimal) | $text`

> $plot

> Display data in plot window. This macro should be the last macro of a command line. The data is read via `STDIN` and consist of a pair of coordinates, with option error values. (`xy, xyex, xyey, xyexe`y) Default dimension is `xy.` The macro is removed from the command line before execution.

> For `$plot(stdin)` only:

> The title, x axis label, and y axis label are assumed to be on the first line of input, delimited with a new-line. However, if the data starts with $`BEGINTEXT`, all text between $`BEGINTEXT` and $`ENDTEXT` will be removed from the data and displayed in a separate text dialog window, with the remaining data, including the title, x axis label, and y axis label, will be displayed in a plot window. Furthermore, if the data contains the string $`ERROR,` an error is assumed to have occurred and a text dialog window is displayed only.

> `Syntax:
> ` `$plot`
> `$plot(,,,)`
> `$plot(<title>,<x axis label>,<y axis label>,[xy|xyex|xyey|xyexey])`
> `$plot(stdin)`
> `Example:
> ` `doit | $plot(This is aTitle,X Axis,Y Axis)
> ` `doit | $plot(stdin)`

> $regions

> Substitute region definition in specified region format, coordinate system, and coordinate format. The default coordinate system is `physical`, default coordinate format `degrees`, and default region format `DS9`. Arguments may appear in any order, as long as they are separated by ',' and no spaces. If one or more properties are specified, only regions with all of the specified properties will be substituted.

> `Syntax:
> ` `$regions`
> `$regions(<options>)`

> where options are one of the following:

> `regions format = [ds9|ciao|saotng|saoimage|pros|xy]`
> `property = [include|exclude|source|background]`
> `coordinate system = [image|physical|detector|amplifier|wcs]`
> `sky frame = [fk4|fk5|icrs|galactic|ecliptic]`
> `sky format = [sexagesimal|degrees]`

> also, the old SAOTNG formats are also supported:

> `$regions_pixels`
> `$regions_degrees`
> `$regions_hms`
> `$include_regions`
> `$include_regions_pixels`
> `$include_regions_degrees`
> `$include_regions_hms`
> `$exclude_regions`
> `$exclude_regions_pixels`
> `$exclude_regions_degrees`
> `$exclude_regions_hms
> `
> `Example:
> ` `dosomething $regions | $text`
> `dosomething $regions(pros) | $text`
> `dosomething $regions(source,wcs,fk5) | $text`
> `dosomething $regions(saotng,background,exclude,ecliptic,sexagesimal) | $text`

> $text

> Display text in a text dialog window. This macro should be the last macro of a command line. To display text from only STDOUT use '|' as the pipe command. To display text from both STDOUT and STDERR, use '|&' as the pipe command. No parameters are required. The macro is removed from the command line before execution.

> `Syntax:
> ` `$text`
> `Example:
> ` `doit | $text # stdout
> doit |& $text # stdout and stderr
> `

> $url

> URLs are processed and stored in a temporary file. Only HTTP and anonymous FTP are supported.

> `Syntax:
> ` `$url(http://<hostname>:<port>/<query>)`
> `$url(ftp://<hostname>/<filename>)`
> `Example:
> ` `$url(http://legacy.gsfc.nasa.gov/rosat/data/p000s26b.img.Z) | uncompress | $image`
> `$url(ftp://legacy.gsfc.nasa.gov/rosat/data/hri/images/rh100193_img.fits) | $image
> `

> $vo_method

> Returns the vo method.

> `Syntax:
> ` `$vo_method`
> `Example:
> ` `echo '$vo_method' | $text`

> $value

> Substitute the value at the location of the cursor of an bind event.

> `Syntax:
> ` `$value
> Example:
> echo "$value" | $text`

> $x
> $y
> $z

> Substitute coordinates of an bind event. When a bind event is triggered, the x,y coordinates of the mouse of the particular data file are returned. The default coordinate system is `physical`. This macro is only available for bind commands. For datacubes, the z coordinate is returned based on the current slice selected.

> `Syntax:
> ` `$x`
> `$x(<coordinate system>,<format>)`
> `$y`
> `$y(<coordinate system>,<format>)
> $z
> $z(<coordinate system>)
> `

> where:

> `coordinate system = [image|physical|detector|amplifier|wcs|wcsa...wcsz]`
> `sky frame = [fk4|fk5|icrs|galactic|ecliptic]`
> `sky format = [hms|sexagesimal|degrees]`
> `Example:
> ` `echo "$x $y" | $text
> echo "$x $y $z" | $text
> echo "$x(fk5,sexagesimal) $y(fk5,sexagesimal)" | $text
> ` `echo "$x(wcs) $y(wcs) $z(wcs)" | $text`

> $xpa

> Returns the xpa access point name.

> `Syntax:
> ` `$xpa`
> `Example:
> ` `echo '$xpa' | $text`

> $xpa_method

> Returns the xpa method.

> `Syntax:
> ` `$xpa_method`
> `Example:
> ` `echo '$xpa_method' | $text`

> Help

> The user may define his own `HELP` message. This message will be available to the user as a menu item. An optional label maybe specified. The default label is `Help`. When invoked, an text dialog window will appear, containing the message. Multiple `HELP` items maybe defined within a menu or across hierarchical menus.

> `Example:`

> > `help Main Help`
> > `A help message may contain`
> > `multiple lines of description of the tasks`
> > `in the menu or menus`
> > `endhelp`

> Parameters

> The user may define his own macros or parameters to be evaluated before the command line is executed. To do this, the user defines a param segment that is referenced in the command line. The param definition has the follow format:

> > `param <name>`
> > `<variable> <entry | checkbox | menu> <title> <default> <{comment}>`
> > `...`
> > `endparam`

> or

> > `param <name>`
> > `@<iraf param filename>`
> > `end`

> The definition either consisted of a number of variables, one per row, or the name of a IRAF style parameter file. DS9 will look for the IRAF parameter file in:

> > `./<filename>`
> > `$UPARM/<filename>`
> > `$HOME/iraf/<filename>`

> `Example:
> `

> > `param foobar`
> > `var1 entry {Variable 1} default {this is a entry}`
> > `var2 checkbox {Variable 2} 1 {this is a checkbox}`
> > `var3 menu {Variable 3} AAA|BBB|CCC {this is a menu}`
> > `endparam`

> To use parameters, specify the param name at the beginning of your command line:

> > `Parameter Test`
> > `*`
> > `menu`
> > `$param(foobar); echo "$var1 $var2 $var3" | $text`

> When the menu item is selected, the user will be presented with a dialog box that contains entry, checkbox, or menu choices for each variable specified. If the user clicks ok, the values are substituted in the command line before execution.

> Hierarchical Menus

> The user may define hierarchical menus. Use this to organized crowded menus. To do this, frame menu entries with `hmenu <label>` and `endhmenu`. Hierarchical menu labels may contain spaces. Multiple levels maybe implemented.

> `Example:
> `

> > `hmenu Stuff`
> > `hello`
> > `*`
> > `menu`
> > `echo "Hello" | $text`

> > `world`
> > `*`
> > `menu`
> > `echo "World" | $text`

> > `hmenu More Stuff`
> > `hello world`
> > `*`
> > `menu`
> > `echo "Hello World" | $text`
> > `endhmenu`
> > `endhmenu`

> Will create an hierarchical menu with two members, `hello` and `world`.

> Sample

> `#
> # Analysis command descriptions:
> # menu label
> # file templates
> # menu/bind
> # analysis command line
> param foo
> var1 entry entry 40 {this is a entry}
> var2 checkbox checkbox 1 {this is a checkbox}
> var3 menu menu AAA|BBB|CCC {this is a menu}
> endparam
> param bar
> @analysis.par
> endparam
> param foobar
> @tvdisply.par
> endparam
> param ltc
> bins entry "Enter number of [t1:t2:]bins" 0 "('0' for default number of bins)"
> endparam
> # Help Main Help
> help Main Help
> These menus contain a test for each possible feature
> supported by the ds9 (blank line above)
> endhelp
> ---
> hmenu Test Web
> help Web Help
> Help for web features
> endhelp
> Web Test url
> *
> web
> http://hea-www.harvard.edu/RD/ds9/
> Web Test file
> *
> web
> file:/home/joye/saods9/ds9/tests/hv.html
> endhmenu
> hmenu Test Basics
> help Basic Help
> Help for basic features
> endhelp
> ---
> Test escape char # this is a comment
> *
> menu
> echo "this is not a macro $$xpa" | $text
> Test pass thru # this is a comment
> *
> menu
> echo "this is not a macro $foo" | $text
> Test $xpa # this is a comment
> *
> menu
> echo $xpa | $text
> Test $xpa_method
> *
> menu
> echo $xpa_method | $text
> ` `
> Test $vo_method
> *
> menu
> echo $vo_method | $text
> ` `Test $filename
> *.fits
> menu
> echo $filename | $text
> Test $filename(root)
> *.fits
> menu
> echo $filename(root) | $text
> Test $xdim $ydim $bitpix
> *.fits
> menu
> echo "$xdim $ydim $bitpix" | $text
> ` `Test $xcen $ycen
> *.fits
> menu
> echo "$xcen $ycen" | $text
> ` `Test $env
> *
> menu
> echo $env(PATH) | $text
> endhmenu
> hmenu Test Regions
> help Regions Help
> Help for regions features
> endhelp
> ---
> Test $regions
> *.fits
> menu
> echo "$regions ds9_s:$regions(ds9,source,image) ciao_b:$regions(ciao,background) saotng_i:$regions(saotng,include,wcs,fk5) pros_e:$regions(pros,exclude,wcs,fk5,sexagesimal) xy_be:$regions(xy,background,exclude,wcs,fk4,hms)" | $text
> Test $regions wcs
> *.fits
> menu
> echo "$regions(ds9,wcs) $regions(ds9,wcs,fk5,sexagesimal) $regions(ds9,wcsa) " | $text
> Test $include_regions_pixels
> *.fits
> menu
> echo "ds9_s: $source_regions ds9_b: $background_regions_pixels ds9_i: $include_regions_degrees ds9_e: $exclude_regions_hms" | $text
> Test $filename $regions
> *.fits
> menu
> echo "$filename[$regions]" | $text
> Test $filename $regions()
> *.fits
> menu
> echo "$filename[$regions()]" | $text
> endhmenu
> hmenu Test Output
> help Output Help
> Help for output features
> endhelp
> ---
> Test $null
> *
> menu
> echo "This is Text" > /dev/null | $null
> Test $text
> *
> menu
> echo "This is Text" | $text
> Test $text stderr
> *
> menu
> ls foofoofoo | $text
> Test $plot
> *
> menu
> cat xy.dat | $plot
> Test $plot(title,x,y,xyey)
> *
> menu
> cat xye.dat | $plot(Title,X Axis,Y Axis,xyey)
> Test $plot(title,x,y,xyexey)
> *
> menu
> cat xyee.dat | $plot(Title,X Axis,Y Axis,xyexey)
> Test $plot(title,x,y,4)
> *
> menu
> cat xyey.dat | $plot(Title,X Axis,Y Axis,4)
> Test $plot(title,x,y,5)
> *
> menu
> cat xyeye.dat | $plot(Title,X Axis,Y Axis,5)
> Test $plot(stdin)
> *
> menu
> cat xye.stdin.dat | $plot(stdin)
> Test $plot(stdin) text
> *
> menu
> cat xye.stdin.text.dat | $plot(stdin)
> Test $plot(stdin) error
> *
> menu
> cat xy.stdin.error.dat | $plot(stdin)
> Test $data
> *.fits
> menu
> $data | $image(new)
> Test $image
> *
> menu
> cat img16.fits | $image
> endhmenu
> hmenu Test Dialogs
> help Dialogs Help
> Help for dialog features
> endhelp
> ---
> Test $message(message)
> *
> menu
> $message(ok,This is a Message) | echo "hello" | $text
> Test $message(ok,message)
> *
> menu
> $message(ok,This is a Message) | echo "World" | $text
> Test $entry(message)
> *
> menu
> echo "$entry(Enter Something)" | $text
> endhmenu
> hmenu Test Params
> help Param Help
> Help for param features
> endhelp
> ---
> Test $param
> *
> menu
> $param(foo); echo "$var1 $var2 $var3" | $text
> Test $param @file
> *
> menu
> $param(bar); echo "$var1 $var2 $var3" | $text
> endhmenu
> hmenu Test Network
> help Network Help
> Help for network features
> endhelp
> ---
> Test $url(http://)
> *
> menu
> $url(http://legacy.gsfc.nasa.gov/FTP/rosat/data/cdrom/vol1/IMAGES/00h/p000s26b.img.Z) | gunzip | $image
> Test $url(ftp://)
> *
> menu
> $url(ftp://legacy.gsfc.nasa.gov/rosat/data/hri/images/fits/rh100193_img.fits) | $image
> Test $geturl $text
> *
> menu
> $geturl(http://hea-www.harvard.edu/RD/saord-cgi/funtools?funcnts+$filename+$regions(source,,)+$regions(background,,))|$text
> Test $geturl $plotstd
> *
> menu
> $param(ltc); $geturl(http://hea-www.harvard.edu/RD/saord-cgi/funtools?funhist_plot+$filename[$regions]+time+$bins)|$plot(stdin)
> endhmenu
> hmenu Test Other
> help Other Help
> Help for other features
> endhelp
> ---
> Test $param @tvdisply
> *
> menu
> $param(foobar); echo "$frame $erase" | $text
> hmenu Test MultiLevel
> test
> *
> menu
> echo "Hello World" | $text
> endhmenu
> endhmenu
> $x $y
> *.fits
> bind x
> echo "$x $y" | $text
> $x(fk5,hms) $y(fk5,hms)
> *.fits
> bind y
> echo "$x(fk5,hms) $y(fk5,hms)" | $text
> $x(wcs,fk5,hms) $y(wcs,fk5,hms)
> *.fits
> bind z
> echo "$x(wcs,fk5,hms) $y(wcs,fk5,hms)" | $text
> `