VolViewerCommandLineArguments

Below is a list of command line arguments supported by the VolViewer application:

General

voldir=XXXXX            //To specify a local directory containing an image stack 
msr=XXXXX              //To specify a local MSR file (measurement geometry object) to load
tfunc=XXXXX            //To specilfy a local TFN file (transfer function) to load
slc=XXXXX               //To specify a local SLC file (clipping planes) to load
auto_close=1           //Tell the application to automatically close once all command line arguments are executed
auto_hide=1            //Tell the application to hide and run in a gui less mode

Movies

movie_rotate(sampling, savefolder, x, y, z, angle)                  //To create a rotation movie from an image

• sampling: is the angle step size
• savefolder: is the folder we wish to save frames to
• x,y,z: either 0 or 1 to enable rotation around that axis
• angle: the angle to rotate about

movie_rock(sampling, savefolder, angle)                               //To create a rock movie from an image 

• sampling: is the angle step size
• savefolder: is the folder we wish to save frames to
• angle: the angle to rock by (+angle to -angle)

Projections

set_view( x, y, z)                                                         //Set the default view of the volume as euler angles
render=1                                                                    //Creates a png of the volume in the root folder

Watchfile

watchfile=XXXXX                                                         //A path to a file to watch

This allows the viewer to be setup to watch a specific ascii file. The file can then contain any of the command line arguments and the program will react to any modification done to this file while launched. This is a simple way to script or interact with the viewer from an external application.

OMERO

omero_server=XXXXX               //To specify the url of an omero server
omero_username=XXXXX          //To specify a username to connect to the omero server
omero_password=XXXXX          //To specify the password for the given username to connect to the omero server
omero_sessionid=XXXXX          //To specify a session id to join on the omero server
omero_port=XXXXX                //To specify the port of the omero server
omero_imageid=XXXXX           //To specify the image id on the omero server we wish to load in volviewer