Slicer3:Slicer Daemon - Revision history

Pieper: /* Server Implementation */

2009-02-10T13:23:01Z

Server Implementation

Pieper: /* Tcl */

2009-02-10T13:11:38Z

Tcl

Pieper: /* Tcl */

2008-11-28T19:43:36Z

Tcl

Pieper: /* Matlab */

2008-09-03T23:36:25Z

Matlab

Pieper: /* Matlab */

2008-09-03T23:35:00Z

Matlab

Klawson at 22:00, 17 June 2007

2007-06-17T22:00:02Z

New page

= 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 '[http://en.wikipedia.org/wiki/Daemon_%28computer_software%29 daemons]'.

= Server Implementation =

The file
[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/SlicerDaemon/Tcl/slicerd.tcl?view=log slicerd.tcl] implements the server side functionality.

By default it listens for connections on port 18943.

= Clients =

== Tcl ==

Two utilities are provided:

* [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/SlicerDaemon/Tcl/slicerget.tcl?view=log slicerget.tcl] is used to read volumes out of slicer. The volume is written to the stdout of the slicerget command in nrrd format.

* [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/SlicerDaemon/Tcl/slicerput.tcl?view=log 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

== Python ==

A [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/SlicerDaemon/Python/ Python based set of code] for interacting with the Slicer Daemon is provided.

For example, the [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/SlicerDaemon/Python/mathExample.py?view=log 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.

<pre>
import slicerd
import numpy

s = slicerd.slicerd()

n = s.get(0)

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

s.put(n, 'newImage')
</pre>

For example, the [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/SlicerDaemon/Python/sliceExample.py?view=log following code] reads a volume and extracts a slice of it for plotting using the matplotlib code (see [http://www.scipy.org the SciPy website] for more info on Python numerics and plotting).

<pre>
import slicerd
import pylab

s = slicerd.slicerd()

n = s.get(0)

slice = n.getImage()[16,:,:]
pylab.imshow(slice)
pylab.show()
</pre>

== Matlab ==

[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/SlicerDaemon/matlab/ Matlab based] versions of Slicer Daemon client code is also under development.

<pre>
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)
</pre>

← Older revision		Revision as of 13:23, 10 February 2009
Line 9:		Line 9:

	By default it listens for connections on port 18943.		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 =		= Clients =

← Older revision		Revision as of 13:11, 10 February 2009
Line 34:		Line 34:

	./Slicer3 --launch xterm		./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 ==		== Python ==

@@ Line 68: / Line 68: @@
 == Matlab ==
-[http://viewvc.slicer.org/Slicer3/trunk/Modules/SlicerDaemon/matlab/ Matlab based] versions of Slicer Daemon client code is also under development.
+[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/SlicerDaemon/Matlab/ Matlab based] versions of Slicer Daemon client code is also under development.
 <pre>

@@ Line 30: / Line 30: @@
   # run an external command and put the data back into slicer
   slicerget.tcl 1 | unu 1op abs -i - slicerput.tcl abs
 == Python ==