Anatomist programming elements

Global and static variables

This is just a subset of some useful variables

Anatomist	singleton class for global state variables
theAnatomist	access to the singleton
Processor	singleton class for commands processor
theProcessor	access to the singleton
Registry	singleton class: list of commands readers and syntax; commands factory
Registry::instance()	access to the singleton
FusionFactory	singleton clas for objects fusion methods; makes a new object from several input ones; tells if it is possible to make a fusion
FusionFactory::instance()	access to the singleton
ObjectReader	singleton class for objects reading; objects factory
ObjectReader::read()	access to the singleton

Configuration options

Anatomist can be customized in a personal options file. This file is located in the .anatomist/config directory of your account and is named settings.cfg (${HOME}/.anatomist/config/settings.cfg on unix).

The configuration file holds the settings selected from the Preferences menu of Anatomist, and may contain additional, “hidden” options which are not (or not yet) accessible via the user interface. It is basicly a list of options with values and the file can have two distinct formats at the moment.

• The “Tree” format variant (older) looks like the following:

*BEGIN TREE anatomist_settings
anatomist_version   1.30alpha
enableUnstable      1
html_browser        konqueror %1 &
*END

• The “Python” format variant (newer) looks like this:

attributes = {
    '__syntax__' : 'anatomist_settings',
    'anatomist_version' : '1.30alpha',
    'enableUnstable' : 1,
    'html_browser' : 'konqueror %1 &',
  }

• In the future this file may move to XML format, but this is only the future.

Python format is more flexible than the older “tree” format because it allows unknown tags. This is important because it keeps compatibility with older anatomist versions: at the moment, new options saved in the settings file will prevent older anatomist versions to read the whole file. Inversely, the python format is only supported (and readable) since Anatomist 1.29.

Options value can take simple types: string, int, float, vector of int…

Here is a complete (I hope) list of the possible options:

Option	Type	Default value	Possible values	Description	Exists since anatomist version
anatomist_version	string			Higher version used	all
axialConvention	string	radio	radio, neuro	Display convention for axial and coronal slices	1.30
boxSelectionColorMode	string	gray	gray, as_selection, custom	When box selection highlighting is enabled (see boxSelectionHighlight), this parameter determines how boxes colors are set. In custom mode, the custom color is given by the boxSelectionCustomColor parameter.	4.2
boxSelectionCustomColor	float_vector	[ 0.7, 0.7, 0.7, 1. ]	RGB (3 float between 0 and 1), or RGBA	When box selection highlighting is enabled (see boxSelectionHighlight), and in custom color mode (see boxSelectionColorMode), this parameter specified the boxes colors.	4.2
boxSelectionIndividual	int	0	0, 1	When box selection highlighting is enabled (see boxSelectionHighlight), this parameter specified whether there is one global box (0) or one box for each selected object (1).	4.2
boxSelectionHighlight	int	1	0, 1	Enables (1) or disables (0) box selection highlighting. Box selection draws a bow around selected objects in seletion control mode. Several parameters control the way bowes are rendered: see boxSelectionIndividual, boxSelectionColorMode, and boxSelectionCustomColor.	4.2
clipBrowserValues	int	0	positive int	Maximum number of characters displayed in graph, nomenclatures and other tree attributes in browsers. 0 means unlimited (default). It may be useful to set a limit here because on some Linux X servers and some Qt implementations, displaying too large text may result in anatomist crashing.	4.0.2
commonScannerBasedReferential	int	0	0, 1	Assumes all "scanner-based" referentials in image headers are the same. By default they are considered all different.	4.2
confirmBeforeQuit	int	1	0, 1	Display or don't display the confirmation box when quittng Anatomist.	4.3
controlWindowLogo	int	1	0, 1	Allows to hide the logo image and (take less space)	all
cursorColor	int_vector	None	RGB (3 ints)	Color of the 3D windows cursor. Only valid if cursorColorAuto is 0	all
cursorColorAuto	int	1	0, 1	In auto mode, a default color is taken and cursorColor is not taken into account	all
cursorShape	string	cross	cross, circle	Shape of the 3D cursor. In Anatomist 1.30, only cross was implemented. In Anatomist 3.0, cursors can be any anatomist object. A number of cursors are available, and users can add their own ones in their .anatomist/cursors directory.	all
cursorSize	int	20	positive int	Size of the 3D cursor (in mm)	all
displayCursorPosition	int	1	0, 1	Display or not the statusbar in 3D windows with the cursor position and image values	4.1
disableOpenGLSelection	int	0	0, 1	Avoid using OpenGL-based selection (in selection control, and 3D windows tooltips). It may be needed with some buggy OpenGL implementations which may cause Anatomist to crash. The "Surface Paint" tool also makes use of it in an unconditional way, so this module might still crash with such an OpenGL implementation.	4.1
displayCursorPosition	int	1	0, 1	Display or not the statusbar in 3D windows with the cursor position and image values	4.1
enableUnstable	int	0	0, 1	Enable or disable unstable and buggy (dangerous) features	1.30
graphDisplayMode	string	meshes	meshes, voxels, all, first	Display mode for 3D objects in graph nodes and relations	all (used since 3.0)
graphHierarchyAttribute	string	name	name, label	Graph nodes attribute used to link and color with nomenclature names	all (used since 3.0)
graphUseHierarchy	int	1	0, 1	enable or disable the coloring of graph 3D elements according to a nomenclature hierarchy	all (used since 3.0)
graphUseToolTips	int	1	0, 1	enable or disable tooltips on 3D views, to display graph nodes labels	all (used since 3.0)
html_browser	string	system dependent		command used to run a HTML borwser for the documentation	all
language	string	system default	en, fr, ...	Translation language in the GUI	all
leftRightDisplayed	int			used only since Anatomist 4.3	all
linkedCursor	int	1	0, 1	Display / hide the 3D cursor	all
listview_background	string	None		Image file to be displayed in "listview" widgets of the GUI: the control window objects and windows lists, browsers etc. This is only a gadget to customize the look of Anatomist. Filenames without an absolute path are taken in the ${HOME}/.anatomist/icons/ directory	all
maxTextureUnitsUsed	int	-1	>= -1	Limit the number of OpenGL texture units used. The default is -1, unlimited. Try this option if you encounter OpenGL rendering problems. Such problems have been seen on Windows machines, where rendering was not performed at all if more than 3 texture units were enabled (even on non-tetured objects).	4.1
path_list	string			Paths list to be inserted in the pre-seelcted directories of file dialogs. It can be useful to reach quickly your favorite data directories	all
selectionColor	int_vector		RGB (3 ints)	Selection color for graph nodes	all
selectionColorInverse	int	0	0, 1	If this option is enabled, the selection color is the negative of the original color of the selected object. In this case, selectionColor is not taken into account	all
selectionRenderingMode	string	ColoredSelection	ColoredSelection, OutlinedSelection	Sets the way selected objects visually appear in 3D renderings. The default, ColoredSelection draws them in a different color (see selectionColor and selectionColorInverse). In OutlinedSelection mode, selected objects don't change color but have a thick outline with the selection color.	3.1.5
useSpmOrigin	int	0	0, 1	If enabled, SPM volumes with an origin are automatically assigned a referential and transformation at load time to take it into account. This used to be the default and only possible behaviour in anatomist 1.29 and previous versions, but as it is often annoying, it has been disabled. When disabled, the same referential can be created via an object-specific option of volumes	1.30
volumeInterpolation	int	1	0, 1	By default, resampled volumes values are interpolated from neighbouring voxels. This gives a nice smooth aspect but is slower and may not let you see the exact limits of the voxels.	all
windowSizeFactor	float	1.5	> 0	Default windows size factor. 1.0 corresponds to 1 pixel for 1mm in data space, larger values means larger windows. Depending on the size and resolution of your screen, you may want to change this default value.	3.0 (default changed from 1. to 1.5 in Anatomist 4.1)
windowsUseGraphicsView	int	0 on MacOS, 1 on other systems	0, 1	When enabled, use a Qt Graphics View as foreground layer in 3D windows: it allows to draw various things on top of the OpenGL renderings, and will be used for visual feedback during interactions, or to display information. It is used for instance for palette contol feedback.	4.4