===================================================== ** Driving AFNI from a Plugout or a Startup Script ** ===================================================== A plugout can control some aspects of AFNI. This is done 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). 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). 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. 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.+ 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. 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. If the specified controller is not open, the acknowledgement from AFNI will be "BAD", otherwise it will be "good". 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". SET_ANATOMY [c.]prefix 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. SET_FUNCTION [c.]prefix Same, but for the functional dataset in controller 'c'. 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). 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 For graph windows, other options available are: matrix=number -> use number sub-graphs (<= 21) pinnum=number -> pin the graph length to number time points 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. If the specified image or graph window is already open, you can still use this command to alter some of its properties. CLOSE_WINDOW [c].windowname Closes a window from controller 'c'. You can only close graph and image viewer windows this way, not plugin windows. 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. N.B.: "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. SETENV name value Set the environment variable "name" to "value" in AFNI; for example SETENV AFNI_CROSSHAIR_LINES YES 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. ============ ** 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. 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, 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