VolViewer Scripting in more detail

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Back to VolViewer overview

See also

MSR file specification MSR file specification (MSR stands for Measure.) MSR files describe 3D objects and are used to pass data between the 3D BanghamLab toolboxes: VolViewer, GFtbox and AAMToolbox.
VolViewerScriptsAPI The VolViewerScriptsAPI enables external applications, such as the AAMToolbox, to exploit VolViewer.

VolViewer scripting and accessing VolViewer from Matlab

VolViewer scripting

A script is a limited form of program - a list of commands. In this case the commands (http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI see VolViewerScriptsAPI]) cover most of the operations that you would usually do interactively. On Windows, VolViewer is an exe file that can either be
interactive, i.e. launched by clicking its icon or from the command prompt using the command


or scripted. In which case the operations (commands) are stored in a script file. In which case VolViewer is launched with

VolViewer set_watchfile('file.txt')

where file.txt contains the commands. For example, if VolViewer is to be a viewing tool for an external program, e.g. a Matlab program, then the file.txt could contain

open_image_stack(0, 'E:\VOLUME DATA\ScanID1934_Leaf1\')

where ScanID1934_Leaf1 is a directory containing a stack of images. VolViewer will automatically load and display these images as soon as it finds that the watchfile has been updated.

Other examples

It is not practical to script VolViewer using these commands manually. It is better to use VolViewer as a tool that is controlled through a library of commands in, for example, Matlab.

Matlab to Volviewer

The DArT_Toolbox contains a library of functions for using and controlling VolViewer from Matlab.