Slicer3:Slicer Daemon

Goals and Functionality

The Slicer Daemon refers to a network protocol that can be used to connect to a running instance of slicer to read and write data in the MRML scene and execute other commands. The name is based on the unix system convention of naming network services 'daemons'.

Server Implementation

The file slicerd.tcl implements the server side functionality.

By default it listens for connections on port 18943.

It is disabled in Slicer3 by default. To enable it, go to the Application Settings dialog (in the View menu) and select the Slicer Settings page. Enable the checkbox for Slicer Daemon and restart slicer.

For each run of slicer, the first connection to the Slicer Daemon will trigger a dialog asking the user to approve the connection.

Clients

Tcl

Two utilities are provided:

• slicerget.tcl is used to read volumes out of slicer. The volume is written to the stdout of the slicerget command in nrrd format.

• slicerput.tcl is used to write volumes into slicer. The volume is read in nrrd format from stdin of slicerput and loaded into the mrml scene.

Some sample commands (assumes your PATH is correctly set to include unu, slicerget and slicerput):

# a noop -- just copy image onto itself
slicerget.tcl 1 | slicerput.tcl noop

# put external data into slicer
unu 1op abs -i d:/data/bunny-small.nrrd | slicerput.tcl

# run an external command and put the data back into slicer
slicerget.tcl 1 | unu 1op abs -i - slicerput.tcl abs

Note: in newer versions of Slicer3 (after mid-November 2008) these commands are available as slicerget and slicerput in the standard path set up by slicer. For example, running the following command will bring up a terminal with the commands available:

./Slicer3 --launch xterm

In the launched xterm, you can run an operation like:

slicerget 0 | unu crop -min 20 20 20  -max 50 50 50 | slicerput cropped

Python

A Python based set of code for interacting with the Slicer Daemon is provided.

For example, the following code reads a volume and creates a new volume where each voxel is the square of the corresponding voxel of the input image. The new image is then sent back to slicer.

import slicerd
import numpy

s = slicerd.slicerd()

n = s.get(0)

im = n.getImage()
n.setImage( im * im )

s.put(n, 'newImage')

For example, the following code reads a volume and extracts a slice of it for plotting using the matplotlib code (see the SciPy website for more info on Python numerics and plotting).

import slicerd
import pylab

s = slicerd.slicerd()

n = s.get(0)

slice = n.getImage()[16,:,:]
pylab.imshow(slice)
pylab.show()

Matlab

Matlab based versions of Slicer Daemon client code is also under development.

function volume = getSlicerVolume( id_or_name )

% This is an example script that shows how to establish a reading pipe to a
% running slicer daemon (start Slicer3 with option --daemon).
% These steps have to be done to adapt the script to your environment:
% - matlab extentions "popenr" and "popenw" have to be compiled for your
%   machine: cd into $SLICER_HOME/Modules/SlicerDaemon/matlab/popen , and
%   do "mex popenr.c" and "mex popenw.c" in matlab.
% - make sure you add the path to popen
% - make sure to add the path to the matlab scripts in 
%   $SLICER_HOME/Modules/SlicerDaemon/Tcl
%
% returns a struct with image data from slicer volume with id "id" or
% name "name" and image information according to the nrrd format.

% add path for popen
cpath = pwd;
cd('popen');
pName = pwd;
addpath (pName);

% find slicerget.tcl script
cd( cpath );
cd('../Tcl');
pScript = pwd;
cd( cpath );

if (isa(id_or_name,'numeric')) 
   % fprintf('The id is: %d.\n',id_or_name);
    cmd_r = sprintf('%s/slicerget.tcl %d',pScript, id_or_name);
elseif (isa(id_or_name,'char'))
   % fprintf('The name is: %s.\n',id_or_name);
    cmd_r = sprintf('%s/slicerget.tcl %s',pScript, id_or_name);
else
    fprintf('Usage: getSlicerVolume(id) or getSlicerVolume(name).\n');
    exit;
end

p_r = popenr(cmd_r);
if p_r < 0
    error(['Error running popenr(',cmd_r,')']);
end

volume = preadNrrd(p_r);

% close pipe
popenr(p_r,-1)