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# qslim

## (Toolbox/qslim.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    [NFV,smf_fname] = qslim(FV,varargin);

### Help Text

    QSLIM - Mesh simplification, wrapper function for Garland's QSLIM executable program
     function [NFV,smf_fname] = qslim(FV,varargin);
     varargin should be entered in pairs '<option>','<arg>'.
     Valid pairs used in this wrapper are:

      '-t', <n>

       Specify the desired number of faces in the simplified model.  You are not
       guaranteed to get exactly the number you ask for, but it should generally
       be within 1-2 faces of the target.

      '-q',[]

       Run quietly.  QSlim will not output the usual status information.

      '-O', <n> (capital O, order)

       Specify the policy for selecting the target position for edge
       contractions.  The following levels of optimization are available:

            3 -- Pick point which minimizes error [default].
            2 -- Pick best point along edge.
            1 -- Pick best of endpoints or midpoint.
            0 -- Pick best of the two endpoints.

      '-m', <penalty>

         Set the penalty for bad meshes (default is 1)

      '-c', <ratio>

         Set the desired compactness ratio (default is 0)

      '-B', <weight>

         Specifies the weight assigned to boundary constraint planes.  The default
         value is currently 1000.  Specify a weight of 0 to disable boundary
         constraints entirely.

      '-W', <n>

         Select the quadric weighting policy.  Available policies are:

            0 -- Weight all quadrics uniformly
            1 -- Weight by area of contributing triangle [default]
            2 -- Weight by angle around vertex

      '-j',[]

         Only perform contractions that do not remove any faces.  You can use this
         feature in conjunction with custom edge sets (see below) to effect a form
         of stitching.  This is not terribly reliable, it's just an experimental
         feature.

      '-F',[]

         This will cause the simplification algorithm to use iterative face
         contraction rather than iterative edge contraction.  Generally speaking,
         this has the following effects:

            - Simplification is faster
            - Less memory is consumed
            - Geometric quality of the results is reduced

      '-o',<fname>

         The output simplified file, default is temp_qslim_out.smf.

     Wrapper option:

        If FV is a string, then that smf file is read, rather than writing out FV to
        a file. Use the -save option below to write the structure FV to a file.
        Saves execution time on subsequent passes

      '-save', <fname>,

         The filename to which to write the structure FV. Default is temp_qslim.smf.

     Defaults are set to -t, 2000, -m, 1000, -o temp_qslime_out.smf

     See http://graphics.cs.uiuc.edu/~garland/software/qslim.html
      http://graphics.cs.uiuc.edu/~garland/research/thesis.html
      for details on QSLIM and dissertation with technical details.

     Examples

     reduce to 2000 faces, with mesh penalty of 1000
     NFV = qslim(FV);

     write the FV to the brain.smf file, return 10,000 faces
     NFV = qslim(FV,'-save','brain.smf','-t',10000);

     load the brain.smf file for the FV information, quiet mode, compactness ratio
     of 1
     NFV = qslim('brain.smf','-q',[],'-c',1);

     See also REDUCEPATCH

### Cross-Reference Information

This function calls

    load_smf                           C:\BrainStorm_2001\Toolbox\load_smf.m
    save_smf                           C:\BrainStorm_2001\Toolbox\save_smf.m

### Listing of function C:\BrainStorm_2001\Toolbox\qslim.m

    function [NFV,smf_fname] = qslim(FV,varargin);
    %QSLIM - Mesh simplification, wrapper function for Garland's QSLIM executable program
    % function [NFV,smf_fname] = qslim(FV,varargin);
    % varargin should be entered in pairs '<option>','<arg>'.
    % Valid pairs used in this wrapper are:
    %
    %  '-t', <n>
    %
    %   Specify the desired number of faces in the simplified model.  You are not
    %   guaranteed to get exactly the number you ask for, but it should generally
    %   be within 1-2 faces of the target.
    %
    %  '-q',[]
    %
    %   Run quietly.  QSlim will not output the usual status information.
    %
    %  '-O', <n> (capital O, order)
    %
    %   Specify the policy for selecting the target position for edge
    %   contractions.  The following levels of optimization are available:
    %
    %        3 -- Pick point which minimizes error [default].
    %        2 -- Pick best point along edge.
    %        1 -- Pick best of endpoints or midpoint.
    %        0 -- Pick best of the two endpoints.
    %
    %  '-m', <penalty>
    %
    %     Set the penalty for bad meshes (default is 1)
    %
    %  '-c', <ratio>
    %
    %     Set the desired compactness ratio (default is 0)
    %
    %  '-B', <weight>
    %
    %     Specifies the weight assigned to boundary constraint planes.  The default
    %     value is currently 1000.  Specify a weight of 0 to disable boundary
    %     constraints entirely.
    %
    %  '-W', <n>
    %
    %     Select the quadric weighting policy.  Available policies are:
    %
    %        0 -- Weight all quadrics uniformly
    %        1 -- Weight by area of contributing triangle [default]
    %        2 -- Weight by angle around vertex
    %
    %  '-j',[]
    %
    %     Only perform contractions that do not remove any faces.  You can use this
    %     feature in conjunction with custom edge sets (see below) to effect a form
    %     of stitching.  This is not terribly reliable, it's just an experimental
    %     feature.
    %
    %  '-F',[]
    %
    %     This will cause the simplification algorithm to use iterative face
    %     contraction rather than iterative edge contraction.  Generally speaking,
    %     this has the following effects:
    %
    %        - Simplification is faster
    %        - Less memory is consumed
    %        - Geometric quality of the results is reduced
    %
    %  '-o',<fname>
    %
    %     The output simplified file, default is temp_qslim_out.smf.
    %
    % Wrapper option:
    %
    %    If FV is a string, then that smf file is read, rather than writing out FV to
    %    a file. Use the -save option below to write the structure FV to a file.
    %    Saves execution time on subsequent passes
    %
    %  '-save', <fname>,
    %
    %     The filename to which to write the structure FV. Default is temp_qslim.smf.
    %
    % Defaults are set to -t, 2000, -m, 1000, -o temp_qslime_out.smf
    %
    % See http://graphics.cs.uiuc.edu/~garland/software/qslim.html
    %  http://graphics.cs.uiuc.edu/~garland/research/thesis.html
    %  for details on QSLIM and dissertation with technical details.
    %
    % Examples
    %
    % reduce to 2000 faces, with mesh penalty of 1000
    % NFV = qslim(FV);
    %
    % write the FV to the brain.smf file, return 10,000 faces
    % NFV = qslim(FV,'-save','brain.smf','-t',10000);
    %
    % load the brain.smf file for the FV information, quiet mode, compactness ratio
    % of 1
    % NFV = qslim('brain.smf','-q',[],'-c',1);
    %
    %
    % See also REDUCEPATCH

    %<autobegin> ---------------------- 26-May-2004 11:34:09 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Utility - General
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\load_smf.m
    %   toolbox\save_smf.m
    %
    % At Check-in: $Author: Mosher $  $Revision: 4 $  $Date: 5/26/04 10:30a $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 24-May-2004
    %
    % Principal Investigators and Developers:
    % ** Richard M. Leahy, PhD, Signal & Image Processing Institute,
    %    University of Southern California, Los Angeles, CA
    % ** John C. Mosher, PhD, Biophysics Group,
    %    Los Alamos National Laboratory, Los Alamos, NM
    % ** Sylvain Baillet, PhD, Cognitive Neuroscience & Brain Imaging Laboratory,
    %    CNRS, Hopital de la Salpetriere, Paris, France
    %
    % See BrainStorm website at http://neuroimage.usc.edu for further information.
    %
    % Copyright (c) 2004 BrainStorm by the University of Southern California
    % This software distributed  under the terms of the GNU General Public License
    % as published by the Free Software Foundation. Further details on the GPL
    % license can be found at http://www.gnu.org/copyleft/gpl.html .
    %
    % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
    % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
    % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
    % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
    % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
    %<autoend> ------------------------ 26-May-2004 11:34:09 -----------------------

    % QSLIM program by
    %
    % Michael Garland
    % Department of Computer Science
    % University of Illinois
    % 201 North Goodwin Avenue
    % Urbana, IL 61801-2302
    %
    % Wrapper author:
    % John C. Mosher

    % ----------------------------- Script History ---------------------------------
    % JCM 24-May-2004  Creation
    % ----------------------------- Script History ---------------------------------

    DEFAULT_INPUT = 'temp_qslim.smf'; % unless the user specifies in FV

    if isstr(FV),
       % user specified an input file instead of a FV structure
       InputFile = FV;
    else
       InputFile = DEFAULT_INPUT; % default
    end

    if ~ispc,
       error(sprintf('Unable to run QSLIM from this %s computer.',computer));
    end

    % where is the QSLIM on this computer
    QSLIM = which('qslim.exe');

    if isempty(QSLIM),
       error(sprintf('Cannot find qslim.exe in the public toolbox'));
    end

    OPERATION = varargin(1:2:end);
    ARGUMENT = varargin(2:2:end);

    if strmatch('-q',OPERATION),
       VERBOSE = 0; % silent running requested
    else
       VERBOSE = 1;
    end

    % setup defaults
    OutputStr = struct('option',[],'arg',[]);

    OutputStr(1).option = '-t'; % wrapper argument
    OutputStr(1).arg = 2000; % number of triangles generated

    OutputStr(2).option = '-o'; % wrapper argument
    OutputStr(2).arg = 'temp_qslim_out.smf'; % default

    OutputStr(3).option = '-m';
    OutputStr(3).arg = 1000; % helps prevent mesh badness

    for i = 1:length(OPERATION),
       % have we already set this output?
       ndx = strmatch(OPERATION{i},{OutputStr.option});
       if isempty(ndx),
          % haven't defined
          % is it valid?
          switch OPERATION{i}
             case {'-O','-B','-W','-t','-F','-o','-I','-m','-c','-r','-M','-q','-j','-h'}
                % okay
                OutputStr(end + 1).option = OPERATION{i};
                OutputStr(end).arg = ARGUMENT{i};
             case '-save'
                InputFile = ARGUMENT{i}; % change the input file specification
             otherwise
                disp(sprintf('unknown qslim option %s',OPERATION{i}))
          end

       else
          % already defined, replace
          OutputStr(ndx).arg = ARGUMENT{i};
       end
    end

    % now make command string

    commandstr = sprintf('"%s"',QSLIM); % initiate the start

    for i = 1:length(OutputStr),
       switch OutputStr(i).option
          case {'-o','-I'}
          % string arg
          commandstr = sprintf(' %s %s %s',commandstr,OutputStr(i).option,OutputStr(i).arg);
       case {'-q','-j','-F','-r','-h'}
          % empty argument
          commandstr = sprintf(' %s %s',commandstr,OutputStr(i).option);
       case {'-B','-W','-t','-m'}
          % assume integer argument
          commandstr = sprintf(' %s %s %.0f',commandstr,OutputStr(i).option,OutputStr(i).arg);
       case {'-c'}
          % floating point argument
          commandstr = sprintf(' %s %s %f',commandstr,OutputStr(i).option,OutputStr(i).arg);
       end
    end

    % where was the output?
    ndx = strmatch('-o',{OutputStr.option});
    OutputFile = OutputStr(ndx).arg;

    commandstr = sprintf('%s %s',commandstr,InputFile); % the input file

    if ~isstr(FV),
       if VERBOSE
          disp(sprintf('Writing out FV to SMF file %s. ..',InputFile))
       end
       save_smf(InputFile,FV);
    end

    if VERBOSE
       disp('Executing . . .')
       disp(commandstr)
    end
    dos(commandstr);
    drawnow

    if VERBOSE
       disp(sprintf('Reading results from %s . . .',OutputFile))
    end

    NFV = load_smf(OutputFile);

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