Description of img2slml

0001 function answer = img2slml( varargin )
0002 % IMG2SLML Trains a generative model of protein subcellular location from a
0003 % collection of microscope images and saves the model as an SLML instance. An SLML model
0004 % consists of four components, a (optional) documentation component, a nuclear pattern model,
0005 % a cell pattern model and a protein pattern model. The input argument param holds the valid
0006 % options for these components.
0007 %
0008 % Arguments                   Description
0009 % ---------                   ------------
0010 % dimensionality              2D/3D
0011 % dnaImagesDirectoryPath      DNA images collection directory
0012 % cellImagesDirectoryPath     Cell images collection directory
0013 % proteinImagesDirectoryPath  Protein images collection directory
0014 % param                       Parameter structure
0015 %
0016 % The shape of param is described
0017 %
0018 % List Of Parameters        Descriptions
0019 % ------------------        ------------
0020 % documentation (optional)
0021 % ------------------------
0022 % This is an optional structure with multiple elements that holds documentation about this model.
0023 %
0024 % documentation.<name>      Holds the value of variable <name>. This is meant to be meta information. Default is empty.
0025 %
0026 % generic model options
0027 % ---------------------
0028 % model.name                (optional) Holds the name of the model. Default is empty.
0029 % model.id                  (optional) Holds the id of the model. Default is empty.
0030 % model.filename            Holds the output filename.
0031 % model.resolution          Model resolution (in microns per pixel). This
0032 %                           the resolution of the dataset used to train the model
0033 % model.downsampling        Downsampling vector used during preprocessing. Default value is
0034 %                           [5 5 1]. Final model resolution will be resolution * downsampling
0035 %                           vector and will be saved in the model as well
0036 %
0037 % nuclear shape model options
0038 % ---------------------------
0039 % nucleus.type              Holds the nuclear model type. Default is "medial axis".
0040 % nucleus.name              (optional) Holds the name of the nuclear model. Default is empty.
0041 % nucleus.id                (optional) Holds the id of the nuclear model. Default is empty.
0042 %
0043 % cell shape model options
0044 % ------------------------
0045 % cell.type                 Holds the cell model type. Default is "ratio".
0046 % cell.name                 (optional) Holds the name of the cell model. Default is empty.
0047 % cell.id                   (optional) Holds the id the cell model. Default is empty.
0048 %
0049 % protein shape model options
0050 % ---------------------------
0051 % protein.type              (optional) Holds the protein model type. The default is "vesicle".
0052 % protein.name              (optional) Holds the name of the protein model. The default is empty.
0053 % protein.id                (optional) Holds the id of the protein model. The default is empty.
0054 % protein.class             Holds the protein class, e.g. lysosome, endosome.
0055 % protein.cytonuclearflag   (optional) Determines whether the protein pattern will be generated in
0056 %                           the cytosolic space ('cyto'), nuclear space ('nuc') or everywhere ('all').
0057 %                           Default is cyto.
0058 %
0059 % other options
0060 % -------------
0061 % verbose                   (optional) Displays messages to screen. Default is true.
0062 % debug                     (optional) Reports errors and warnings. Default is false.
0063 % train.flag                (optional) Selects what model is going to be trained ('nuclear',
0064 %                           'framework', or 'all'). Default is 'all'.
0065 % masks                     (optional) A string with
0066 
0067 % Author: Ivan E. Cao-Berg (icaoberg@cmu.edu)
0068 %
0069 % Copyright (C) 2007-2013 Murphy Lab
0070 % Lane Center for Computational Biology
0071 % School of Computer Science
0072 % Carnegie Mellon University
0073 %
0074 % March 9, 2012 I. Cao-Berg Added documentation and updated license file
0075 % March 9, 2012 I. Cao-Berg Added new input argument list for CellOrganizer but also
0076 %               kept backward compatibility with SLML Toolbox
0077 % March 9, 2012 I. Cao-Berg Removed output argument model.
0078 % March 28, 2012 I. Cao-Berg Added a control structure under which if img2model returns
0079 %                            an empty model structure, the method exits
0080 % March 28, 2012 I. Cao-Berg Removed saving of temporary models for debugging purposes and
0081 %                            added backward compatibility mode message to screen
0082 % March 28, 2012 I. Cao-Berg Added verification of input arguments when running in compatibility
0083 %                            mode (compatible with SLML Tools)
0084 % March 28, 2012 I. Cao-Berg Added verification of input arguments when running in default
0085 %                            mode (CellOrganizer)
0086 % April 11, 2012 I. Cao-Berg Added debug flag to parameter structure and set the default value
0087 %                            to false
0088 % April 17, 2012 I. Cao-Berg Added cytonuclearflag to the protein model
0089 % July 3, 2012   M. Mackie   Added train.flag to the parameter structure
0090 %                            with the default value of 'all'
0091 % July 5, 2012 I. Cao-Berg   Fixed a bug where the default value was not set properly
0092 % July 9, 2012 I. Cao-Berg   Updated code so that when debug flag is set true, it saves the model as a mat file
0093 %                            Fixed bug that replaced the model.id and model.name to the default values
0094 %                            Updated code to include all possible options of the input parameter structure
0095 % Nov 9, 2012 D. Sullivan    Fixed bug in the param try catch that set
0096 %                            model.cellShapeModel.type to param.nucleus.type instead of param.cell.type
0097 % Jan 20, 2013 I. Cao-Berg   Removed examples 1 and 2 from documentation.
0098 %                            Users should refer to demos for examples.
0099 % Jan 28, 2013 I. Cao-Berg   Updated method so that models are saved as mat
0100 %                            files instead of XML models
0101 % Jan 30, 2013 I. Cao-Berg   Updated code so that parameter display is
0102 %                            always false
0103 % Feb. 1, 2013 I. Cao-Berg   Method requires model resolution as part of
0104 %                            the parameter structure
0105 % Feb 22, 2013 D. Sullivan   Changed call to img2model to accept the
0106 %                            updated param structure
0107 % Feb 24, 2013 D. Sullivan   Added param.model.protein_resolution from
0108 %                            param.model.original_resolution so it can be
0109 %                            adjusted later.
0110 % May 2, 2013 I. Cao-Berg    Fixed method so that it uses default value
0111 %                            when param.train.flag not recognized
0112 % May 9, 2013 I. Cao-Berg    Updated method so that if will save the
0113 %                            metadata of the model iff a model exists. This prevents inclusion of
0114 %                            empty model fields
0115 % May 17, 2013 I. Cao-Berg   Updated methods so that they will save empty fields to SLML instance
0116 %
0117 % This program is free software; you can redistribute it and/or modify
0118 % it under the terms of the GNU General Public License as published
0119 % by the Free Software Foundation; either version 2 of the License,
0120 % or (at your option) any later version.
0121 %
0122 % This program is distributed in the hope that it will be useful, but
0123 % WITHOUT ANY WARRANTY; without even the implied warranty of
0124 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
0125 % General Public License for more details.
0126 %
0127 % You should have received a copy of the GNU General Public License
0128 % along with this program; if not, write to the Free Software
0129 % Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
0130 % 02110-1301, USA.
0131 %
0132 % For additional information visit http://murphylab.web.cmu.edu or
0133 % send email to murphy@cmu.edu
0134 
0135 %icaoberg 7/3/2013
0136 answer = false;
0137 
0138 %icaoberg moved upward so it is accesible to all methods
0139 
0140 %checks the contents of the structure holding the parameters
0141 try
0142     param = varargin{5};
0143     if ~isa( param, 'struct' )
0144         warning('CellOrganizer: Input parameter list must be a structure.');
0145     end
0146     param.slml.level = '1';
0147     param.slml.version = '1.1';
0148 catch
0149     param = [];
0150     param.slml.level = '1';
0151     param.slml.version = '1.1';
0152     param.display = false;
0153     param.debug = false;
0154     param.verbose = true;
0155 end
0156 
0157 try
0158     verbose = param.verbose;
0159     if ~isa( verbose, 'logical' )
0160         verbose = true;
0161     end
0162 catch
0163     verbose = true;
0164 end
0165 
0166 %D. Sullivan 6/4/13 fixed assignment mismatch bug-verbose was being set
0167 %instead of display
0168 try
0169     display = param.display;
0170     if ~isa( display, 'logical' )
0171         dislpay = false;
0172     end
0173 catch
0174     display = false;
0175     param.display = display;
0176 end
0177 
0178 try
0179     debug = param.debug;
0180     if ~isa( debug, 'logical' )
0181         param.debug = false;
0182         debug = false;
0183     end
0184 catch
0185     param.debug = false;
0186     debug = false;
0187 end
0188 
0189 %CHECK INPUT ARGUMENTS
0190 if length(varargin) == 5
0191     %icaoberg march 28, 2012
0192     dimensionality = varargin{1};
0193     if ~(strcmpi( dimensionality, '2d' ) || ...
0194             strcmpi( dimensionality, '3d' ))
0195         
0196         %icaoberg 7/3/2013
0197         warning('Unrecognized or unsupported dimensionality. Exiting method.');
0198         return
0199     else
0200         %icaoberg 9/16/2013
0201         param.dimensionality = dimensionality;
0202     end
0203     
0204     dnaImagesDirectoryPath = varargin{2};
0205     cellImagesDirectoryPath = varargin{3};
0206     proteinImagesDirectoryPath = varargin{4};
0207     
0208     %check the contents of param.model
0209     try
0210         temp = param.model.name;
0211         %icaoberg 7/9/2012
0212         if ~isa( temp, 'char' )
0213             warning(['CellOrganizer: Optional input argument param.model.name must be a string. ' ...
0214                 'Changing to default value']);
0215             param.model.name = '';
0216         end
0217     catch
0218         param.model.name = '';
0219     end
0220     
0221     try
0222         temp = param.model.id;
0223         %icaoberg 7/9/2012
0224         if ~isa( temp, 'char' )
0225             warning(['CellOrganizer: Optional input argument param.model.id must be a string. ' ...
0226                 'Changing to default value']);
0227             param.model.id = '';
0228         end
0229     catch
0230         param.model.id = '';
0231     end
0232     
0233     %icaoberg 06/02/2013
0234     try
0235         downsampling = param.model.downsampling;
0236     catch
0237         if strcmpi( dimensionality, '3D' )
0238             downsampling = [5 5 1];
0239         else
0240             downsampling = [1 1];
0241         end
0242     end
0243     
0244     % model.resolution
0245     try
0246         param.model.original_resolution = param.model.resolution;
0247         %D. Sullivan 2/24/13 added param.model.protein_resolution
0248         param.model.protein_resolution = param.model.original_resolution;
0249         
0250         param.model.downsampling = downsampling;
0251         param.model.resolution = param.model.resolution .* downsampling;
0252         clear downsampling
0253     catch
0254         disp('Model resolution not set. Exiting method.');
0255         
0256         answer = false;
0257         return
0258     end
0259     
0260     try
0261         temp = param.model.filename;
0262         if ~isa( temp, 'char' )
0263             error('CellOrganizer: Input parameter filename must be a string.');
0264         end
0265     catch err
0266         error( 'CellOrganizer: Unable to set output filename' );
0267     end
0268     
0269     %check the contents of param.nucleus, param.cell and param.protein
0270     compartments = { 'nucleus', 'cell', 'protein' };
0271     fields = { 'type', 'name', 'id' };
0272     for c=1:1:length(compartments)
0273         compartment = [ 'param.' compartments{c} ];
0274         for f=1:1:length(fields)
0275             field = [ compartment '.' fields{f} ];
0276             try
0277                 eval(['temp=' field ';']);
0278                 if ~isa( temp, 'char' )
0279                     eval([field '=''''' ';']);
0280                 end
0281             catch
0282                 eval([field '=''''' ';']);
0283             end
0284         end
0285     end
0286     
0287     try
0288         documentation = param.documentation;
0289         if ~isa( documentation, 'struct' )
0290             error('CellOrganizer: Documentation must be a structure.');
0291         end
0292     catch
0293         param.documentation = [];
0294     end
0295     
0296     %mmackie july 3, 2012
0297     %checking the training flag
0298     try
0299         trainFlag = param.train.flag;
0300         if ~isa( trainFlag, 'char' );
0301             error('CellOrganizer: training flag must be a string');
0302         end
0303     catch
0304         param.train.flag = 'all';
0305         %icaoberg july 5, 2012
0306         trainFlag = param.train.flag;
0307     end
0308     
0309     %icaoberg july 5, 2012
0310     if ~strcmpi( trainFlag, 'nuclear') && ...
0311             ~strcmpi( trainFlag, 'framework') && ...
0312             ~strcmpi( trainFlag, 'all')
0313         if debug
0314             disp('CellOrganizer: unrecognized training flag. Using default value.');
0315         end
0316         trainFlag = 'all';
0317     end
0318     
0319 elseif length(varargin) == 10
0320     %icaoberg march 28, 2012
0321     if verbose
0322         fprintf( 1, '%s', 'Entering backward compatibility mode' );
0323     end
0324     
0325     dimensionality = varargin{1};
0326     if ~strcmpi( dimensionality, '2D' ) || ...
0327             ~strcmpi( dimensionality, '3D' )
0328         error('CellOrganizer: Unknown or unsupported dimensionality');
0329     end
0330     
0331     dnaImagesDirectoryPath = varargin{2};
0332     if ~exist( dnaImagesDirectory, 'dir' )
0333         error('CellOrganizer: DNA images directory does not exist.')
0334     end
0335     
0336     cellImagesDirectoryPath = varargin{3};
0337     if ~exist( cellImagesDirectory, 'dir' )
0338         error('CellOrganizer: Cell images directory does not exist.')
0339     end
0340     
0341     proteinImagesDirectoryPath = varargin{4};
0342     if ~exist( proteinImagesDirectory, 'dir' )
0343         error('CellOrganizer: Protein images directory does not exist.')
0344     end
0345     
0346     modelName = varargin{5};
0347     if ~isa( modelName, 'char' )
0348         error('CellOrganizer: Model name must be a string.');
0349     end
0350     
0351     cellName = varargin{6};
0352     if ~isa( cellName, 'char' )
0353         error('CellOrganizer: Cell name must be a string.');
0354     end
0355     
0356     compartmentName = varargin{7};
0357     if ~isa( compartmentName, 'char' )
0358         error('CellOrganizer: Compartment name must be a string.');
0359     end
0360     
0361     proteinName = varargin{8};
0362     if ~isa( proteinName, 'char' )
0363         error('CellOrganizer: Protein name must be a string.');
0364     end
0365     
0366     documentation = varargin{9};
0367     if isempty( documentation )
0368         warning('CellOrganizer: Documentation is empty.');
0369     elseif ~isa( documentation, 'struct' )
0370         error('CellOrganizer: Documentation must be a structure');
0371     end
0372     
0373     filename = varargin{10};
0374     if isempty( filename )
0375         error( 'CellOrganizer: Filename for output SLML instance cannot be empty.');
0376     elseif ~isa( filename, 'char' );
0377         error( 'CellOrganizer: Filename for output SLML instance must be a string.');
0378     end
0379 else
0380     %there can only be 5 or 10 input arguments
0381     error('CellOrganizer: Wrong number of input arguments.');
0382 end
0383 
0384 if verbose
0385     fprintf( 1, '%s\n', 'Checking the existence of temporary folder' );
0386 end
0387 
0388 dimensionality = varargin{1};
0389 
0390 %TRAIN THE GENERATIVE MODEL
0391 if strcmpi( dimensionality, '2D' )
0392     % Train a generative model from a set of images
0393     model = img2model( dimensionality, ...
0394         dnaImagesDirectoryPath, ...
0395         cellImagesDirectoryPath, ...
0396         proteinImagesDirectoryPath, param );
0397     
0398     %icaoberg march 28, 2012
0399     if isempty( model )
0400         disp('CellOrganizer: img2model returned an empty model. Exiting program.')
0401         return
0402     end
0403 elseif strcmpi( dimensionality, '3D' )
0404     
0405     %D. Sullivan, 2/22/13 changed varargin{5} to updated param structure
0406     %D. Sullivan 5/3/13 changed varargin{2}-nuc to varargin{3}-cell so that
0407     %nuclear holefinding will still work
0408     %     model = img2model( dimensionality, varargin{2},...
0409     %         param );
0410     dnaImagesDirectoryPath = varargin{2};
0411     cellImagesDirectoryPath = varargin{3};
0412     proteinImagesDirectoryPath = varargin{4};
0413     
0414     model = img2model( dimensionality, ...
0415         dnaImagesDirectoryPath, ...
0416         cellImagesDirectoryPath, ...
0417         proteinImagesDirectoryPath, ...
0418         param );
0419     
0420     %icaoberg march 28, 2012
0421     if isempty( model )
0422         warning( ['CellOrganizer: img2model returned an empty model. ' ...
0423             'Exiting program.']);
0424         return
0425     end
0426 else
0427     error(['CellOrganizer: Unknown dimensionality ' dimensionality ]);
0428 end
0429 
0430 %PARSE GENERATIVE MODEL INTO SLML INSTANCE
0431 filename = param.model.filename;
0432 if strcmpi( dimensionality, '2D' );
0433     % Convert the trained model into SLML format
0434     
0435     %model2slml( model, modelName, cellName, ...
0436     %    compartmentName, proteinName, ...
0437     %    documentation, filename );
0438     %July 27, 2012 Y.Yu Added the dimensionality field to the model
0439     if ~isfield(model,'dimensionality')
0440         model.dimensionality = '2D';
0441     end
0442     
0443     %July 27, 2012 Y.Yu Used the new model2slml method to save slml file
0444     %model2slml( model, filename );
0445     
0446     % model.name                (optional) Holds the name of the model. Default is empty.
0447     try
0448         if ~isempty( param.model.name )
0449             model.name = param.model.name;
0450         end
0451     catch
0452         if debug
0453             disp('Model name not set. Ignoring meta data field.')
0454         end
0455     end
0456     
0457     % model.id                  (optional) Holds the id of the model. Default is empty.
0458     try
0459         if ~isempty( param.model.id )
0460             model.id = param.model.id;
0461         end
0462     catch
0463         
0464         if debug
0465             disp('Model ID not set. Ignoring meta data field.')
0466         end
0467     end
0468     
0469     % model.filename            Holds the output filename.
0470     try
0471         if ~isempty( param.model.filename )
0472             model.filename = param.model.filename;
0473         end
0474     catch
0475         
0476         if debug
0477             disp('Model filename not set. Ignoring meta data field.')
0478         end
0479     end
0480     
0481     % nucleus
0482     % nucleus.name              (optional) Holds the name of the nuclear model. Default is empty.
0483     try
0484         if ~isempty( param.nucleus.name )
0485             model.nuclearShapeModel.name = param.nucleus.name;
0486         end
0487     catch
0488         if debug
0489             disp('Nuclear shape model name not set. Ignoring meta data field.')
0490         end
0491     end
0492     
0493     % nucleus.id                (optional) Holds the id of the nuclear model. Default is empty.
0494     try
0495         if ~isempty( param.nucleus.id )
0496             model.nuclearShapeModel.id = param.nucleus.id;
0497         end
0498     catch
0499         if debug
0500             disp('Nuclear shape model ID not set. Ignoring meta data field.')
0501         end
0502     end
0503     
0504     % nucleus.type              Holds the nuclear model type. Default is "medial axis"
0505     try
0506         if ~isempty( param.nucleus.type )
0507             model.nuclearShapeModel.type = param.nucleus.type;
0508         else
0509              model.nuclearShapeModel.type = 'medial axis';
0510         end
0511     catch
0512         if debug
0513             disp('Nuclear shape model type not set. Using default: medial axis.')
0514             model.nuclearShapeModel.type = 'medial axis';
0515         end
0516     end
0517     
0518     %at this point the param.model.resolution has been checked and is not
0519     %empty and it exists
0520     model.nuclearShapeModel.resolution = param.model.resolution;
0521     
0522     % cell
0523     % cell.name                 (optional) Holds the name of the cell model. Default is empty.
0524     if strcmpi( param.train.flag, 'framework' ) || strcmpi( param.train.flag, 'all' )
0525         try
0526             if ~isempty( param.cell.name )
0527                 model.cellShapeModel.name = param.cell.name;
0528             end
0529         catch
0530             if debug
0531                 disp('Cell shape model name not set. Ignoring meta data field.')
0532             end
0533         end
0534         
0535         % cell.id                   (optional) Holds the id the cell model. Default is empty.
0536         try
0537             if ~isempty( param.cell.id )
0538                 model.cellShapeModel.id = param.cell.id;
0539             end
0540         catch
0541             if debug
0542                 disp('Cell shape model ID not set. Ignoring meta data field.')
0543             end
0544         end
0545         
0546         % cell.type                 Holds the cell model type. Default is "ratio".
0547         try
0548             %DPS 11/9/12 fixed bug setting model.cellShapeModel.type to nucleuse
0549             %instead of cell.
0550             if ~isempty( para.cell.type )
0551                 model.cellShapeModel.type = param.cell.type;
0552             else
0553                 model.cellShapeModel.type = 'ratio';
0554             end
0555         catch
0556             if debug
0557                 disp('Cell shape model type not set. Using default: ratio.')
0558                 model.cellShapeModel.type = 'ratio';
0559             end
0560         end
0561         
0562         %at this point the param.model.resolution has been checked and is not
0563         %empty and it exists
0564         model.cellShapeModel.resolution = param.model.resolution;
0565     end
0566     
0567     % protein
0568     % protein.name              (optional) Holds the name of the protein model. The default is empty.
0569     if strcmpi( param.train.flag, 'all' )
0570         try
0571             if ~isempty( param.protein.name )
0572                 model.proteinModel.name = param.protein.name;
0573             end
0574         catch
0575             if debug
0576                 disp('Protein shape model name not set. Ignoring meta data field.')
0577             end
0578         end
0579         
0580         % protein.id  (optional) Holds the id of the protein model. The default is empty.
0581         try
0582             if ~isempty( param.protein.id )
0583                 model.proteinModel.id = param.protein.id;
0584             end
0585         catch
0586             if debug
0587                 disp('Protein shape model ID not set. Ignoring meta data field.')
0588             end
0589         end
0590         
0591         % protein.type              (optional) Holds the protein model type. The default is "vesicle".
0592         try
0593             if ~isempty( param.protein.type )
0594                 model.proteinModel.type = param.protein.type;
0595             end
0596         catch
0597             if debug
0598                 disp('Protein shape model type not set. Using default: vesicle.')
0599                 model.proteinModel.type = 'vesicle';
0600             end
0601         end
0602         
0603         %at this point the param.model.resolution has been checked and is not
0604         %empty and it exists
0605         model.proteinModel.resolution = param.model.resolution;
0606      end
0607     
0608     %icaoberg 9/10/2013
0609     %this helper method transforms the files in the temporary folder into
0610     %intermediate results
0611     disp( 'Building intermediate results' );
0612     make_intermediate_results_from_temp_folder( param );
0613     
0614     %icaoberg 9/10/2013
0615     %removes temp folder if debug set to true
0616     if ~debug
0617         disp( 'Removing temporary folder' );
0618         rmdir( [ pwd filesep 'temp' ], 's'  );
0619     end
0620     
0621     %July 26, 2012 Y.Yu Save the result as mat file instead of xml file
0622     save( [filename(1:end-3) 'mat'], 'model' );
0623     answer = true;
0624 else
0625     % Conversion of the trained model into SLML format
0626     % unsupported for 3D models in the current version.
0627     model.dimensionality = dimensionality;
0628     
0629     % model.name                (optional) Holds the name of the model. Default is empty.
0630     try
0631         model.name = param.model.name;
0632     catch
0633         if debug
0634             disp('Model name not set. Ignoring meta data field.')
0635         end
0636     end
0637     
0638     % model.id                  (optional) Holds the id of the model. Default is empty.
0639     try
0640         model.id = param.model.id;
0641     catch
0642         if debug
0643             disp('Model ID not set. Ignoring meta data field.')
0644         end
0645     end
0646     
0647     % model.filename            Holds the output filename.
0648     try
0649         model.filename = param.model.filename;
0650     catch
0651         if debug
0652             disp('Model filename not set. Ignoring meta data field.')
0653         end
0654     end
0655     
0656     % nucleus
0657     % nucleus.name              (optional) Holds the name of the nuclear model. Default is empty.
0658     try
0659         model.nuclearShapeModel.name = param.nucleus.name;
0660     catch
0661         if debug
0662             disp('Nuclear shape model name not set. Ignoring meta data field.')
0663         end
0664     end
0665     
0666     
0667     % nucleus.id                (optional) Holds the id of the nuclear model. Default is empty.
0668     try
0669         model.nuclearShapeModel.id = param.nucleus.id;
0670     catch
0671         if debug
0672             disp('Nuclear shape model ID not set. Ignoring meta data field.')
0673         end
0674     end
0675     
0676     % nucleus.type              Holds the nuclear model type. Default is "medial axis"
0677     try
0678         model.nuclearShapeModel.type = param.nucleus.type;
0679     catch
0680         if debug
0681             disp('Nuclear shape model type not set. Using default: medial axis.')
0682             model.nuclearShapeModel.type = 'medial axis';
0683         end
0684     end
0685     
0686     if strcmpi( trainFlag, 'framework' ) || strcmpi( trainFlag, 'all' )
0687         % cell
0688         % cell.name                 (optional) Holds the name of the cell model. Default is empty.
0689         try
0690             model.cellShapeModel.name = param.cell.name;
0691         catch
0692             if debug
0693                 disp('Cell shape model name not set. Ignoring meta data field.')
0694             end
0695         end
0696         
0697         % cell.id                   (optional) Holds the id the cell model. Default is empty.
0698         try
0699             model.cellShapeModel.id = param.cell.id;
0700         catch
0701             if debug
0702                 disp('Cell shape model ID not set. Ignoring meta data field.')
0703             end
0704         end
0705         
0706         % cell.type                 Holds the cell model type. Default is "ratio".
0707         try
0708             %DPS 11/9/12 fixed bug setting model.cellShapeModel.type to nucleuse
0709             %instead of cell.
0710             model.cellShapeModel.type = param.cell.type;
0711         catch
0712             if debug
0713                 disp('Cell shape model type not set. Using default: ratio.')
0714                 model.cellShapeModel.type = 'ratio';
0715             end
0716         end
0717     end
0718     
0719     if strcmpi( trainFlag, 'all' )
0720         % protein
0721         % protein.name              (optional) Holds the name of the protein model. The default is empty.
0722         try
0723             if isfield( param.protein, 'name' ) && ~isempty( param.protein.name )
0724                 model.proteinShape.name = param.protein.name;
0725             end
0726         catch
0727             if debug
0728                 disp('Protein shape model name not set. Ignoring meta data field.')
0729             end
0730         end
0731         
0732         % protein.id  (optional) Holds the id of the protein model. The default is empty.
0733         try
0734             model.proteinShape.id = param.protein.id;
0735         catch
0736             if debug
0737                 disp('Protein shape model ID not set. Ignoring meta data field.')
0738             end
0739         end
0740         
0741         % protein.type              (optional) Holds the protein model type. The default is "vesicle".
0742         try
0743             model.proteinShape.type = param.protein.type;
0744         catch
0745             if debug
0746                 disp('Protein shape model type not set. Using default: vesicle.')
0747                 model.proteinShapeModel.type = 'vesicle';
0748             end
0749         end
0750         
0751         % protein.class             Holds the protein class, e.g. lysosome, endosome.
0752         try
0753             model.proteinShape.class = param.protein.class;
0754         catch
0755             if debug
0756                 disp('Protein shape model class not set. Ignoring meta data field.')
0757             end
0758         end
0759         
0760         % protein.cytonuclearflag   (optional) Determines whether the protein pattern will be generated in
0761         %                           the cytosolic space ('cyto'), nuclear space ('nuc') or everywhere ('all').
0762         %                           Default is cyto.
0763         try
0764             flag = param.protein.cytonuclearflag;
0765             if ~strcmpi( flag, 'cyto' ) && ~strcmpi( flag, 'nuc' ) ...
0766                     ... & ~strcmpi( flag, 'all' )
0767                     if debug
0768                     warning('Protein shape model cytonuclear flag is unrecognized. Using default: cyto.');
0769                     end
0770                     flag = 'cyto';
0771             end
0772             
0773             model.proteinShape.cytonuclearflag = flag;
0774             clear flag;
0775         catch
0776             if debug
0777                 warning( 'Protein shape model cytonuclear flag not set. Using default: cyto.');
0778             end
0779             model.proteinShape.cytonuclearflag = 'cyto';
0780         end
0781         
0782         %set model dimensionality
0783         model.proteinShape.dimensionality = dimensionality;
0784         
0785         %D. Sullivan 2/24/13
0786         %There are no assumptions of similar resolution, therefore there
0787         %must be separate resolutions tracked for framework and protein
0788         model.nuclearShapeModel.resolution = param.model.resolution;
0789         model.cellShapeModel.resolution = param.model.resolution;
0790     end
0791     
0792     try
0793         model.documentation = param.documentation;
0794         model.documentation.date = date;
0795     catch
0796         model.documentation.date = date;
0797     end
0798     
0799     %icaoberg 9/10/2013
0800     %this helper method transforms the files in the temporary folder into
0801     %intermediate results
0802     make_intermediate_results_from_temp_folder( param );
0803     
0804     %icaoberg 9/10/2013
0805     %removes temp folder if debug set to true
0806     if ~debug
0807         disp( 'Removing temporary folder' );
0808         rmdir( [ pwd filesep 'temp' ], 's'  );
0809     end
0810     
0811     %icaoberg 1/28/2012
0812     save( [filename(1:end-3) 'mat'], 'model' );
0813     answer = true;
0814 end%3D
0815 end%img2slml
img2slml

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SOURCE CODE
