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| − | = Goals and Functionality =
| + | <big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:Slicer_Daemon here]</font></big> |
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| − | 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]'.
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| − | = Server Implementation =
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| − | The file
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| − | [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/SlicerDaemon/Tcl/slicerd.tcl?view=log slicerd.tcl] implements the server side functionality.
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| − | By default it listens for connections on port 18943.
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| − | | |
| − | = Clients =
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| − | == Tcl ==
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| − | Two utilities are provided:
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| − | * [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.
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| − | * [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.
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| − | Some sample commands (assumes your PATH is correctly set to include unu, slicerget and slicerput):
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| − | # a noop -- just copy image onto itself
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| − | slicerget.tcl 1 | slicerput.tcl noop
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| − | # put external data into slicer
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| − | unu 1op abs -i d:/data/bunny-small.nrrd | slicerput.tcl
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| − | # run an external command and put the data back into slicer
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| − | slicerget.tcl 1 | unu 1op abs -i - slicerput.tcl abs
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| − | == Python ==
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| − | 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.
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| − | 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.
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| − | <pre>
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| − | import slicerd
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| − | import numpy
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| − | s = slicerd.slicerd()
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| − | n = s.get(0)
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| − | im = n.getImage()
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| − | n.setImage( im * im )
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| − | s.put(n, 'newImage')
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| − | </pre>
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| − | 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).
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| − | <pre>
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| − | import slicerd
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| − | import pylab
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| − | s = slicerd.slicerd()
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| − | n = s.get(0)
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| − | slice = n.getImage()[16,:,:]
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| − | pylab.imshow(slice)
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| − | pylab.show()
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| − | </pre> | |
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| − | == Matlab ==
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| − | [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/SlicerDaemon/matlab/ Matlab based] versions of Slicer Daemon client code is also under development.
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| − | <pre>
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| − | function volume = getSlicerVolume( id_or_name )
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| − | % This is an example script that shows how to establish a reading pipe to a
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| − | % running slicer daemon (start Slicer3 with option --daemon).
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| − | % These steps have to be done to adapt the script to your environment:
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| − | % - matlab extentions "popenr" and "popenw" have to be compiled for your
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| − | % machine: cd into $SLICER_HOME/Modules/SlicerDaemon/matlab/popen , and
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| − | % do "mex popenr.c" and "mex popenw.c" in matlab.
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| − | % - make sure you add the path to popen
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| − | % - make sure to add the path to the matlab scripts in
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| − | % $SLICER_HOME/Modules/SlicerDaemon/Tcl
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| − | %
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| − | % returns a struct with image data from slicer volume with id "id" or
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| − | % name "name" and image information according to the nrrd format.
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| − | % add path for popen
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| − | cpath = pwd;
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| − | cd('popen');
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| − | pName = pwd;
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| − | addpath (pName);
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| − | % find slicerget.tcl script
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| − | cd( cpath );
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| − | cd('../Tcl');
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| − | pScript = pwd;
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| − | cd( cpath );
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| − | if (isa(id_or_name,'numeric'))
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| − | % fprintf('The id is: %d.\n',id_or_name);
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| − | cmd_r = sprintf('%s/slicerget.tcl %d',pScript, id_or_name);
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| − | elseif (isa(id_or_name,'char'))
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| − | % fprintf('The name is: %s.\n',id_or_name);
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| − | cmd_r = sprintf('%s/slicerget.tcl %s',pScript, id_or_name);
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| − | else
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| − | fprintf('Usage: getSlicerVolume(id) or getSlicerVolume(name).\n');
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| − | exit;
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| − | end
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| − | p_r = popenr(cmd_r);
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| − | if p_r < 0
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| − | error(['Error running popenr(',cmd_r,')']);
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| − | end
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| − | volume = preadNrrd(p_r);
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| − | % close pipe
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| − | popenr(p_r,-1)
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| − | </pre> | |
