===================================================== *** Driving AFNI from a Plugout or a Startup Script *** ===================================================== An external program (i.e., a "plugout") can control some aspects of AFNI. This functionality is invoked by passing a command line of the form DRIVE_AFNI command arguments ... to AFNI (once the plugout connection is open, of course). The commands available are described below. The sample plugout plugout_drive.c can be used to test how things work (highly recommended before you start writing your own code). A startup Script (file ".afni.startup_script") can also give a sequence of commands to be run immediately after AFNI starts up. The file consists of a sequence of command lines (without the "DRIVE_AFNI" prefix). It is also possible to read in a Script file using the "Datamode->Misc->Run Script" button from the AFNI controller. Some of the current state of AFNI can be saved to ".afni.startup_script" using the "Datamode->Misc->Save Layout" button (by giving a blank as the filename -- or any filename containing the string "script" -- other filenames produce a 'layout' description which is intended to be included in your .afnirc file). You can also give commands to AFNI on the 'afni' command line, using the '-com' option. For example: afni -com 'OPEN_WINDOW A.axialimage' \ -com 'SWITCH_UNDERLAY anat' \ -com 'SAVE_JPEG A.axialimage sss.jpg' \ -com 'QUIT' \ somedirectory could be used to create an image file 'sss.jpg' automatically. The AFNI GUI would open up (and so X11 must be running), but no user interaction would actually occur -- the image opens and gets saved, and then AFNI just ends. N.B.: If the 'QUIT' command weren't included above, AFNI would remain open, ready for user interaction after the image file was saved. ============================================================================== A programmer of a plugin can register a command string and a callback function to be called when that command string is 'driven' to AFNI. For example: static int junkfun( char *cmd ) { fprintf(stderr,"junkfun('%s')\n",cmd) ; return 0 ; } AFNI_driver_register( "JUNK" , junkfun ) ; If the callback function return value is negative, a warning message will be printed to stderr; otherwise, the return value is ignored. The string that is passed to the callback function is everything AFTER the initial command and the blank(s) that follows; in the above example, if "JUNK elvis lives" were the driver command, then junkfun is called with the string "elvis lives". In a plugin, the logical place to put the call to AFNI_driver_register() is in the PLUGIN_init() function. If you call AFNI_driver_register() with a new command name that duplicates an existing one, then an error message is printed to stderr and this call will be ignored. For this reason, you may want to prefix your commands with some identifier; for example, a hypothetical diffusion tensor analysis plugin could give command names starting with "DTI_". Or perhaps use your institution's name or your initials as a prefix, as in "NIMH_" or "RWC_". ============================================================================= COMMANDS (in no coherent order) ------------------------------- ADD_OVERLAY_COLOR colordef colorlab Adds the color defined by the string "colordef" to the list of overlay colors. It will appear in the menus with the label "colordef". Example: ADD_OVERLAY_COLOR #ff5599 pinkish SET_THRESHOLD [c.]val [dec] Sets the threshold slider for controller index 'c' (default='A') to level ".val" (a number between .0000 and .9999, inclusive). If the optional 'dec' parameter is set, this is a number between 0 and 4 (inclusive) setting the power-of-ten factor for the slider. Example: SET_THRESHOLD A.3000 2 will set the '**' (decimal) level of the slider to 2 and the slider value to 30 (=0.3000*100). ++ You can also use "SET_FUNC_THRESH" for the command name. SET_THRESHNEW [c] val [flags] Sets the threshold slider for controller index 'c' (default='A') to the numerical value 'val', which must be in the range [0..9999]. If the optional 'flags' string contains the character '*', then the slider decimal offset (i.e., the '**' setting) will be changed to match the size of 'val'. If 'flags' contains the character 'p', then 'val will be interepreted as a p-value (and so must be between 0.0 and 1.0). Examples: SET_THRESHNEW A 9.2731 SET_THRESHNEW B 0.3971 *p SET_PBAR_NUMBER [c.]num Sets the number of panes in the color pbar to 'num' (currently must be between 2 and 20, inclusive). Example: SET_PBAR_NUMBER A.10 SET_PBAR_SIGN [c.]+ or [c.]- Sets the color pbar to be positive-only (+) or signed (-). Example: SET_PBAR_SIGN A.+ SET_PBAR_ALL [c.]{+|-}num val=color val=color ... Sets all color pbar parameters at once; The initial string specifies the controller ('A', 'B', etc.), the sign condition of the pbar ('+' or '-') and the number of panes to setup. 'num' equations of the form 'val=color' follow the initial string; these set up the top levels and colors of each pane. Example: SET_PBAR_ALL A.+5 2.0=yellow 1.5=green 1.0=blue 0.5=red 0.2=none The top pane runs from 2.0-1.5 and is yellow; the second pane runs from 1.5-1.0 and is blue, etc. The 'color' values must be legal color labels. SET_PBAR_ALL [c.]{+|-}99 topval colorscale_name [options] Sets the color pbar for controller #c to be in "continuous" colorscale mode. Again, '+' or '-' is used to specify if the colorscale should be positive-only or signed. The special value of 99 panes is used to indicate colorscale mode. The number 'topval' tells the scale value to go at the top of the colorscale. The string 'colorscale_name' tells which colorscale to use. For example: SET_PBAR_ALL A.+99 1.0 Color_circle_AJJ The 'options' available at this time only apply when in this "continuous" colorscale case. They are ROTA=n => after loading the colorscale, rotate it by 'n' steps FLIP => after loading the colorscale, flip it upside down These options are part of how the AFNI_PBAR_LOCK function works, and probably aren't relevant for manual use. PBAR_ROTATE [c.]{+|-} Rotates the color pbar in the positive ('+') or negative ('-') direction: PBAR_ROTATE A.+ DEFINE_COLORSCALE name number=color number=color ... or DEFINE_COLORSCALE name color color color Defines a new colorscale with the given name. The format of the following arguments is either like "1.0=#ffff00" or like "#ff00ff" (all must be in the same format). See http://afni.nimh.nih.gov/afni/afni_colorscale.html for more information about the format of color names and about how the colorscale definition works. ++ You can also use "DEFINE_COLOR_SCALE" for the command name. SET_FUNC_AUTORANGE [c.]{+|-} Sets the function "autoRange" toggle to be on ('+') or off ('-'): SET_FUNC_AUTORANGE A.+ SET_FUNC_RANGE [c.]value Sets the functional range to 'value'. If value is 0, this turns autoRange on; if value is positive, this turns autoRange off: SET_FUNC_RANGE A.0.3333 SET_FUNC_VISIBLE [c.]{+|-} Turns the "See Overlay" toggle on or off: SET_FUNC_VISIBLE A.+ You can also use SEE_OVERLAY for this, which is closer to the label on the GUI button. SEE_OVERLAY Same as SET_FUNC_VISIBLE SET_FUNC_RESAM [c.]{NN|Li|Cu|Bk}[.{NN|Li|Cu|Bk}] Sets the functional resampling mode: SET_FUNC_RESAM A.Li.Li sets the func and threshold resampling modes both to Linear interpolation. OPEN_PANEL [c.]Panel_Name Opens the specified controller panel, where 'Panel_Name' is one of 'Define_Overlay', 'Define_Datamode', or 'Define_Markers'. At this time, there is no way to close a panel except from the GUI. SYSTEM command string Executes "command string" using the system() library function; for example, "SYSTEM mkdir aaa". CHDIR newdirectory Changes the current directory; for example, "CHDIR aaa". This is the directory into which saved files (e.g., images) will be written. RESCAN_THIS [c] rescans the current session directory for controller 'c', where 'c' is one of 'A', 'B', 'C', 'D', or 'E'. If 'c' is absent, the 'A' controller's current session is scanned. SET_SESSION [c.]directoryname Switches controller 'c' to be looking at the named directory. The match on directory names is done by a sub-string match - that is, directoryname = "fred" will match an AFNI session directory named "wilhelm/frederick/von/guttenstein". ++ You can also use "SWITCH_SESSION" or "SWITCH_DIRECTORY" for the command. SET_VIEW [c.]view Switches controller 'c' to the named "view", which can be one of 'orig', 'acpc' or 'tlrc'. The underlay dataset must have an appropriate transformation. SET_ANATOMY [c.]prefix [i] Switches controller 'c' to be looking at the anatomical dataset with the given prefix. The prefix must be a perfect match - this is NOT a sub-string match. ++ If an optional integer is given (separated by a space) after the prefix, this is the sub-brick index to view. ++ You can also use "SWITCH_ANATOMY" or "SWITCH_UNDERLAY" for the command. ++ The 'prefix' can also be the dataset IDcode string, if you insist. SET_FUNCTION [c.]prefix [j [k]] Same, but for the functional dataset in controller 'c'. ++ If an optional integer is given (separated by a space) after the prefix, this is the sub-brick index to view as the 'OLay'; if a second integer is given, this is the sub-brick index to use as the 'Thr'. ++ You can also use "SWITCH_FUNCTION" or "SWITCH_OVERLAY" for the command. SET_SUBBRICKS [c] i j k Without switching underlay or overlay datasets, change the sub-bricks being viewed in the viewer specified by the initial letter. Index i = underlay sub-brick (grayscale) Index j = overlay sub-brick for 'Olay' (color) Index k = overlay sub-brick for 'Thr' (threshold) For example, "SET_SUBBRICKS B 33 -1 44" will set the underlay sub-brick to 33, the threshold sub-brick to 44, and will not change the color sub-brick (since -1 is not a legal value). ++ You can also use "SET_SUB_BRICKS" for the command name. OPEN_WINDOW [c.]windowname [options] Opens a window from controller 'c'. The window name can be one of axialimage sagittalimage coronalimage axialgraph sagittalgraph coronalgraph If the specified controller is not yet opened, it will be opened first (like pressing the 'New' button). If the command is of the form "OPEN_WINDOW c", then only the controller itself will be opened. For all windows, one allowed option is: geom=PxQ+R+S or geom=PxQ or geom=+R+S to make the window be PxQ pixels in size and located at screen coordinates (R,S). Another option for both graph and image windows is keypress=c -> where 'c' is a single character to send as if the user pressed that key in the specified window ++ multiple keypress= options can be used, but each one can only send one keystroke; example: "keypress=Z keypress=Z" to zoom in twice in an image viewer. For image windows, other options available are: ifrac=number -> set image fraction in window to number (<= 1.0) mont=PxQ:R -> montage P across, Q down, every R'th slice opacity=X -> where X is from 0..9 crop=x1:x2,y1:y2 -> crop images from voxels x1 to x2, and y1 to y2 (inclusive) -- mostly for use in .afni.startup_script; use x1=x2=0 and y1=y2=0 to turn cropping off. For graph windows, other options available are: matrix=number -> use 'number' sub-graphs (<= 21) pinnum=number -> pin the graph length to 'number' time points pinbot=a pintop=b -> pin the graph time window to run from 'a..b' You can also open plugin windows with a windowname like so: A.plugin.buttonlabel where buttonlabel is the plugin's button label with blanks replaced by underscores or hyphens (e.g., Render_Dataset). You can also use the geom=+R+S option with this type of window opening, to position the plugin interface window. There is no way to control any other settings in the plugin interface (e.g., pre-set some fields). If the specified image or graph window is already open, you can still use this command to alter some of its properties. ++ You can also use "ALTER_WINDOW" for the command name, which makes more sense if you are using this to apply some change to an already open viewer window. CLOSE_WINDOW [c.]windowname Closes a window from controller 'c'. You can only close graph and image viewer windows this way, not plugin windows. SAVE_JPEG [c.]windowname filename Save a JPEG dump of the given window to 'filename' (using the cjpeg filter, which must be in the path). The windowname can be one of 'axialimage', 'sagittalimage', 'coronalimage', 'axialgraph', 'sagittalgraph', or 'coronalgraph'. If the filename does not end in the string ".jpg" or ".JPG", then ".jpg" will be appended. ++ Saving is done via the cjpeg program, which must be in the path, and is included in the standard AFNI source and binary collections. ++ If the dataset has non-square voxels, then the default method of saving images will produce non-square pixels (as extracted from the dataset) -- this will make the images look peculiar when you open them later. To avoid this peculiarity, set environment variable AFNI_IMAGE_SAVESQUARE to YES (cf. SETENV below). This comment applies to all image SAVE_* commands below, except for SAVE_RAW* (where AFNI_IMAGE_SAVESQUARE has no effect). SAVE_PNG [c.]windowname filename Like SAVE_JPEG, but saves to the lossless PNG format. ++ Saving is done via the pnmtopng filter, which must be in the path. Unlike cjpeg, this program is NOT part of the AFNI collection, but must be installed separately (usually by getting the NETPBM package). SAVE_FILTERED [c.]windowname filtercommand Like SAVE_JPEG or SAVE_PNG, but instead of a filename, you give a Unix filter that processes a PPM file. For example SAVE_FILTERED axialimage 'pnmcut 10 20 120 240 | pnmtopng > zork.png' will crop the image and save it into a PNG file. You'll need to become familiar with the NETPBM package if you want to use this command. ++ As indicated in the example, you'll need to put filtercommand in quotes if it contains blanks, which it almost surely will. Other filter examples: Save to a PPM file: 'cat > zork.ppm' Save to a TIFF file: 'ppm2tiff -c none > zork.tif' SAVE_ALLJPEG [c].imagewindowname filename SAVE_ALLPNG [c].imagewindowname filename SAVE_MPEG [c].imagewindowname filename SAVE_AGIF [c].imagewindowname filename Save ALL the images in the given image sequence viewer (either as a series of JPEG/PNG files, or as one animation file). The windowname can be one of 'axialimage', 'sagittalimage', or 'coronalimage'. Do NOT put a suffix like '.jpg' or '.mpg' on the filename -- it will be added. ++ Unlike 'SAVE_JPEG', these commands do not work with graph windows. SAVE_RAW [c.]imagewindowname filename Saves the raw data from the given image viewer to a file. This data is the slice data extracted from the dataset, not further processed in any way (unlike the other SAVE_* image options, which convert the slice data to grayscale or colors). This output file contains only the data, with no header of any sort indicating the dimensions of the image or the actual type of data stored therein. SAVE_RAWMONT [c.]imagewindowname filename Saves the raw data from the given image viewer to a file, AS MONTAGED. (The montage gap is ignored.) Same as 'SAVE_RAW' if the montage isn't on. SET_DICOM_XYZ [c] x y z SET_SPM_XYZ [c] x y z SET_IJK [c] i j k Set the controller coordinates to the given triple; DICOM_XYZ has the coordinates in DICOM (RAI) order, SPM_XYZ has the coordinates in SPM (LPI) order, and IJK has voxel indexes instead of spatial coordinates. SET_XHAIRS [c.]code Set the crosshairs ('Xhairs') control to the specified value, where 'code' is one of the following strings: OFF SINGLE MULTI LR_AP LR_IS AP_IS LR AP IS READ_NIML_FILE fname Reads the NIML-formatted file 'fname' from disk and processes it as if the data in the file had been sent to AFNI through a TCP/IP socket. PURGE_MEMORY [dataset_prefix] If no prefix is given, the sub-bricks of all datasets will be purged from memory, and when re-used, AFNI will re-read them from disk. If a prefix is given, only that dataset (in all coordinate views) will be purged. ++ "Locked" datasets will not be purged -- a dataset will be locked into memory if it can't be re-read from disk (e.g., was sent from SUMA; is being drawn upon, nudged, or acquired in realtime; was loaded from a '3dcalc()' command line call; or was fetched across the Web). QUIT AFNI will exit immediately. Communication with the dead being difficult, this action forestalls all further attempts to send commands to AFNI. SETENV name value Set the environment variable "name" to "value" in AFNI; for example SETENV AFNI_CROSSHAIR_LINES YES SETENV AFNI_IMAGE_SAVESQUARE YES Most of the time, when you set an environment variable inside AFNI, just changing the variable won't have any immediate visible effect. Only when you instigate something that this variable controls will anything change in AFNI. Thus, you may want to 'REDISPLAY' afterwards. GETENV name Get the value of environment variable "name", and print to the terminal. For example: GETENV AFNI_PLUGINPATH would show the directory that plugins were loaded from, if set: AFNI_PLUGINPATH = /home/elvis/abin If a variable is not set, the output says as much: AFNI_PLUGINPATH = REDISPLAY Forces all images and graphs to be redrawn. SLEEP ms Causes AFNI to sleep for "ms" milliseconds. The main use would be in a script file to provide a pause between some effects. QUIET_PLUGOUTS Turns off normal plugout communications messages NOISY_PLUGOUTS Turns on normal plugout communication messages TRACE {YES | NO} Turns debug tracing on or off. Mostly for AFNI developers. ============================================================================== ** GRAPHS ** ============ The following commands are used to open graph windows and manipulate them. These commands don't actually interact with the rest of AFNI - they are really just using AFNI as a graph display server. [This functionality was added per the request of Jerzy Bodurka at the NIH, to provide a way to graph physiological signals monitored while the subject is in the scanner, at the same time the EPI images are being sent to the AFNI realtime plugin.] At present there are two similar kinds of graphs: XY = connected (x,y) pairs - you must supply (x,y) for each new point 1D = x increments by 1 each time, so you only give y for each new point; when x overflows past the right boundary, it wraps back to x=0. Each graph can have multiple sub-graphs, which are stacked up vertically with separate y axes and a common x axis (sub-graph #1 at the bottom, etc.). Label strings in the graphs are interpreted in a TeX-like fashion. In particular, an underscore means to start a subscript and a circumflex means to start a superscript. Subscript or superscripts that are more than one character long can be grouped using curly {braces}. Greek letters and other special characters can be included using TeX-like escapes. For example, "time (\Delta t=0.1)" might be a good label for the x-axis of a 1D graph. The full list of such escapes is \Plus \Cross \Diamond \Box \FDiamond \FBox \FPlus \FCross \Burst \Octagon \alpha \beta \gamma \delta \epsilon \zeta \eta \theta \iota \kappa \lambda \mu \nu \xi \omicron \pi \rho \sigma \tau \upsilon \phi \chi \psi \omega \Alpha \Beta \Gamma \Delta \Epsilon \Zeta \Eta \Theta \Iota \Kappa \Lambda \Mu \Nu \Xi \Omicron \Pi \Rho \Sigma \Tau \Upsilon \Phi \Chi \Psi \Omega \propto \int \times \div \approx \partial \cap \langle \rangle \ddagger \pm \leq \S \hbar \lambar \cup \degree \nabla \downarrow \leftarrow \rightarrow \leftrightarrow \oint \in \notin \surd \cents \bar \exists \geq \forall \subset \oplus \otimes \dagger \neq \supset \infty \uparrow \{ \} \\ \_ \? All characters are drawn with line strokes from an internal font; standard fonts (e.g., Helvetica) are not available. If you want classier looking graphs, stop whining and find another program. -------------------------- OPEN_GRAPH_XY gname toplab xbot xtop xlab ny ybot ytop ylab nam_1 .. nam_ny This opens a graph window for graphing non-MRI data. Each graph window has a gname string; this lets you graph into more than one window. Other arguments are toplab = string to graph at top of graph [empty] xbot = numerical minimum of x-axis in graph [0] xtop = numerical maximum of x-axis in graph [1] xlab = string to graph below x-axis [empty] ny = number of sub-graphs (all share same x-axis) [1] ybot = numerical minimum of y-axis in graph [0] ytop = numerical maximum of y-axis in graph [1] ylab = string to graph to left of y-axis [empty] nam_1 = name to plot at right of sub-graph 1, etc. [not plotted] Arguments are separated by spaces. If a label has a space in it, you can put the label inside "double" or 'single' quote characters. If you don't want a particular label plotted, make it the empty string "" or ''. If you don't want names plotted at the right of sub-graphs, stop the arguments at ylab. Only the gname argument is strictly required - the other arguments have default values, which are given in [brackets] above. CLOSE_GRAPH_XY gname Closes the graph window with the given name. CLEAR_GRAPH_XY gname Clears the graph out of the given window (leaves the axes and labels). ADDTO_GRAPH_XY gname x y_1 y_2 .. y_ny [repeat] Actually plots data into the given window. In the i-th sub-graph, a line will be drawn connecting to (x,y_i), for i=1..ny. You can put many sets of points on the line, subject to the limitation that a plugout command line cannot contain more than 64 Kbytes. -------------------------- OPEN_GRAPH_1D gname toplab nx dx xlab ny ybot ytop ylab nam_1 .. nam_ny Opens a graph window that is set up to plot nx points across with spacing dx, in ny separate sub-graphs. When the graph is full, the graph recycles back to the beginning. The meaning and [default] values of parameters are: toplab = string to graph at top of graph [empty] nx = number of points along the x-axis [500] dx = spacing between x-axis points [1] xlab = string to graph below x-axis [empty] ny = number of sub-graphs (all share same x-axis) [1] ybot = numerical minimum of y-axis in graph [0] ytop = numerical maximum of y-axis in graph [1] ylab = string to graph to left of y-axis [empty] nam_1 = name to plot at right of sub-graph 1, etc. [not plotted] CLOSE_GRAPH_1D gname Closes the graph window with the given name. CLEAR_GRAPH_1D gname Clears the graph out of the given window (leaves the axes and labels). ADDTO_GRAPH_1D gname y_1 y_2 .. y_ny [repeat] Actually plots data into the given window. You can put many sets of ny values at a time on the command line, subject to the limitation that a plugout command line cannot contain more than 64 Kbytes. Also, if you put more than nx sets of values, only the first nx will be plotted, since that will fill up the graph through one full cycle. -------------------------- SET_GRAPH_GEOM gname geom=X-geometry-string This lets you move/resize a graph (1D or XY). X-geometry-string is one of the forms: 300x100 = set window size to 300 pixels wide, 100 high +50+90 = set window location to 50 pixels across, 90 down 300x100+50+90 = set window size and location at the same time