SLML2IMG Synthesizes an instance from a collection
of SLML Level 1.0 Version 1.* models.
instances may be saved in the following forms:
Tiff stacks = a 3D tiff image stack for each pattern generated using the input models
indexed images = a single 3D tiff image stack where each pattern is represented by a number 1-n
object mesh = a .obj mesh file for each pattern generated using the input models (blenderfile option)
SBML-Spatial file = a systems biology markup language(SBML) formatted xml file utilizing the spatial extension in level 3 version 1
COMMENT: When the method is not deployed the shape of the input arguments is
slml2img( models, param )
List Of Input Arguments Descriptions
----------------------- ------------
models A cell array of filenames
param A structure holding the function options
The shape of param is described
List Of Parameters Descriptions
------------------ ------------
targetDirectory (optional) Directory where the images are going to be saved. Default is current directory.
prefix (optional) Filename prefix for the synthesized images. Default is 'demo'
numberOfSynthesizedImages (optional) Number of synthesized images. Default is 1.
compression (optional) Compression of tiff, i.e. 'none', 'lzw' and 'packbits'
debug (optional) Keeps temporary results and catches errors with full reports
display (optional) Display flag for figures
verbose (optional) Print the intermediate steps to screen. Default is true.
microscope (optional) Microscope model from which we select a point spread function. Default is 'none'
synthesis (optional) Synthesis parameter that allows to
synthesize 'nucleus', 'framework' or 'all'. Default is 'all'
protein.cytonuclearflag (optional) Defines the allowable region for protein placement.
The default is the cytonuclearflag included in the model.
sampling.method (optional) Can be 'disc' or 'sampled'. Default is trimmed
savePDF (optional) Saves the probability density function for a given pattern during 2D synthesis. Default is False.
spherical_cell (optional) Boolean flag that indicates whether a cell is spherical. Default is False.
synthesis.diffeomorphic.maximum_iterations (optional) Integer defining the maximum number of iterations during diffeo inference. Default is 100.
randomwalk (optional) Boolean flag of whether to perform a shape space walk. Default is False.
framefolder (optional) The folder in which to look for completed frames and save finished frames from the diffeomorphic synthesis.
The default is './frames/'.
walksteps (optional) The integer number of steps to walk during a shape space walk. Default is 1.
walk_type (optional) Type of random walk to perform. Default is 'willmore'.
overlapsubsize (optional) Defines the downsampling fraction to perform during object overlap avoidance. Default is 0.3.
overlapthresh (optional) Defines the amount of overlap that is allowed between objects. Default is 1.
rendAtStd (optional) Defines the number of standard deviations to render gaussian objects at. Default is 2.
sampling.method.density (optional) An integer. Default is empty.
protein.cytonuclearflag (optional) Can 'cyto', 'nucleus' or 'all'. Default is all.
resolution.cell (optional) The resolution of the cell and nucleus that are being passed in
resolution.objects (optional) The resolution of the object model being synthesized
instance.cell (optional) A binary cell image to be filled with objects. Default is empty.
instance.nucleus (optional) A binary nuclear image to be filled with objects. Default is empty.
image_size (optional) The image size. Default is [1024 1024] for both 2D and 3D in x and y
spherical_cell (optional) Indicates whether the cell is spherical or not. Default is FALSE
output.tifimages (optional) boolean flag specifying whether to write out tif images
output.indexedimage (optional) boolean flag specifying whether to write out indexed image
output.blenderfile (optional) boolean flag specifying whether to write out (.obj) files for use in blender
output.blender.downsample (optional) downsampling fraction for the creation of object files (1 means no downsampling, 1/5 means 1/5 the size)
output.SBML (optional) boolean flag specifying whether to write out (.xml) files with SBML-Spatial representations of geometries
Example
-------
instances = { 'model01.xml', 'model02.mat', 'model03.mat' };
param.targetDirectory = pwd;
param.prefix = 'demo'
param.numberOfSynthesizedImages = 100;
param.compression = 'lzw';
param.microscope = 'svi';
param.verbose = true;
>> slml2img( instances, param );0001 function answer = slml2img( varargin ) 0002 % SLML2IMG Synthesizes an instance from a collection 0003 % of SLML Level 1.0 Version 1.* models. 0004 % instances may be saved in the following forms: 0005 % Tiff stacks = a 3D tiff image stack for each pattern generated using the input models 0006 % indexed images = a single 3D tiff image stack where each pattern is represented by a number 1-n 0007 % object mesh = a .obj mesh file for each pattern generated using the input models (blenderfile option) 0008 % SBML-Spatial file = a systems biology markup language(SBML) formatted xml file utilizing the spatial extension in level 3 version 1 0009 % 0010 % 0011 % COMMENT: When the method is not deployed the shape of the input arguments is 0012 % slml2img( models, param ) 0013 % 0014 % List Of Input Arguments Descriptions 0015 % ----------------------- ------------ 0016 % models A cell array of filenames 0017 % param A structure holding the function options 0018 % 0019 % The shape of param is described 0020 % 0021 % List Of Parameters Descriptions 0022 % ------------------ ------------ 0023 % targetDirectory (optional) Directory where the images are going to be saved. Default is current directory. 0024 % prefix (optional) Filename prefix for the synthesized images. Default is 'demo' 0025 % numberOfSynthesizedImages (optional) Number of synthesized images. Default is 1. 0026 % compression (optional) Compression of tiff, i.e. 'none', 'lzw' and 'packbits' 0027 % debug (optional) Keeps temporary results and catches errors with full reports 0028 % display (optional) Display flag for figures 0029 % verbose (optional) Print the intermediate steps to screen. Default is true. 0030 % microscope (optional) Microscope model from which we select a point spread function. Default is 'none' 0031 % synthesis (optional) Synthesis parameter that allows to 0032 % synthesize 'nucleus', 'framework' or 'all'. Default is 'all' 0033 % protein.cytonuclearflag (optional) Defines the allowable region for protein placement. 0034 % The default is the cytonuclearflag included in the model. 0035 % sampling.method (optional) Can be 'disc' or 'sampled'. Default is trimmed 0036 % savePDF (optional) Saves the probability density function for a given pattern during 2D synthesis. Default is False. 0037 % spherical_cell (optional) Boolean flag that indicates whether a cell is spherical. Default is False. 0038 % synthesis.diffeomorphic.maximum_iterations (optional) Integer defining the maximum number of iterations during diffeo inference. Default is 100. 0039 % randomwalk (optional) Boolean flag of whether to perform a shape space walk. Default is False. 0040 % framefolder (optional) The folder in which to look for completed frames and save finished frames from the diffeomorphic synthesis. 0041 % The default is './frames/'. 0042 % walksteps (optional) The integer number of steps to walk during a shape space walk. Default is 1. 0043 % walk_type (optional) Type of random walk to perform. Default is 'willmore'. 0044 % overlapsubsize (optional) Defines the downsampling fraction to perform during object overlap avoidance. Default is 0.3. 0045 % overlapthresh (optional) Defines the amount of overlap that is allowed between objects. Default is 1. 0046 % rendAtStd (optional) Defines the number of standard deviations to render gaussian objects at. Default is 2. 0047 % sampling.method.density (optional) An integer. Default is empty. 0048 % protein.cytonuclearflag (optional) Can 'cyto', 'nucleus' or 'all'. Default is all. 0049 % resolution.cell (optional) The resolution of the cell and nucleus that are being passed in 0050 % resolution.objects (optional) The resolution of the object model being synthesized 0051 % instance.cell (optional) A binary cell image to be filled with objects. Default is empty. 0052 % instance.nucleus (optional) A binary nuclear image to be filled with objects. Default is empty. 0053 % image_size (optional) The image size. Default is [1024 1024] for both 2D and 3D in x and y 0054 % spherical_cell (optional) Indicates whether the cell is spherical or not. Default is FALSE 0055 % 0056 % output.tifimages (optional) boolean flag specifying whether to write out tif images 0057 % output.indexedimage (optional) boolean flag specifying whether to write out indexed image 0058 % output.blenderfile (optional) boolean flag specifying whether to write out (.obj) files for use in blender 0059 % output.blender.downsample (optional) downsampling fraction for the creation of object files (1 means no downsampling, 1/5 means 1/5 the size) 0060 % output.SBML (optional) boolean flag specifying whether to write out (.xml) files with SBML-Spatial representations of geometries 0061 % 0062 % Example 0063 % ------- 0064 % instances = { 'model01.xml', 'model02.mat', 'model03.mat' }; 0065 % param.targetDirectory = pwd; 0066 % param.prefix = 'demo' 0067 % param.numberOfSynthesizedImages = 100; 0068 % param.compression = 'lzw'; 0069 % param.microscope = 'svi'; 0070 % param.verbose = true; 0071 % 0072 % >> slml2img( instances, param ); 0073 0074 % Author: Ivan E. Cao-Berg (icaoberg@cmu.edu) 0075 % Created: May 8, 2007 0076 % March 7, 2012 R.F.Murphy Don't create directory to hold 3D images if 0077 % generating 2D 0078 % March 8, 2012 I. Cao-Berg Documented the method 0079 % March 9, 2012 I. Cao-Berg Changed disp to fprintf and improved logs 0080 % March 9, 2012 I. Cao-Berg Removed print of progress bar from log file 0081 % March 21, 2012 I. Cao-Berg Changed protein.location to protein.cytonuclearflag 0082 % April 11, 2012 I. Cao-Berg Removed removal of temporary folder 0083 % June 5, 2012 M. Mackie Added option to save as an index image using 0084 % param.image.type and param.image.option 0085 % June 6, 2012 M. Mackie Removed parameter image.option (index images 0086 % may only be saved as 'priority' 0087 % July 25, 2012 D. Sullivan Added fields param.blender.file and param.blender.downsample 0088 % Created option for saving .obj files for exporting to blender 0089 % July 26, 2012 D. Sullivan Changed param.image and param.blender structures 0090 % to param.output structure (see header for usage) 0091 % July 30, 2012 I. Cao-Berg Modified code that is res files in the temporary folder rather than 0092 % the folder itself. This way if a user trains a model and synthesizes 0093 % images in the same script, the temp folder remains intact in case it is 0094 % run in debug mode 0095 % August 20, 2012 I. Cao-Berg Renamed img2blender to im2blender 0096 % October 1, 2012 I. Cao-Berg Removed deprecated code from previous versions 0097 % October 9, 2012 I. Cao-Berg Added print of the error stack if method 0098 % fails to synthesize an image 0099 % January 28, 2012 I. Cao-Berg Updated try/catch statement to print an 0100 % error report when running debug mode 0101 % April 29, 2013 D. Sullivan added documentation for param.debug 0102 % May 18, 2013 I . Cao-Berg Updated method so if framework fails to 0103 % synthesize it returns an empty framework 0104 % June 7, 2013 R. Arepally added the variable shiftvector as a parameter to 0105 % the im2blender function. This fixes the bug of inconsistant shifting of 0106 % different objects when the blender files are created. 0107 % July 23, 2013 D. Sullivan added primitives type of output 0108 0109 % Copyright (C) 2007-2013 Murphy Lab 0110 % Carnegie Mellon University 0111 % 0112 % This program is free software; you can redistribute it and/or modify 0113 % it under the terms of the GNU General Public License as published 0114 % by the Free Software Foundation; either version 2 of the License, 0115 % or (at your option) any later version. 0116 % 0117 % This program is distributed in the hope that it will be useful, but 0118 % WITHOUT ANY WARRANTY; without even the implied warranty of 0119 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 0120 % General Public License for more details. 0121 % 0122 % You should have received a copy of the GNU General Public License 0123 % along with this program; if not, write to the Free Software 0124 % Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 0125 % 02110-1301, USA. 0126 % 0127 % For additional information visit http://murphylab.web.cmu.edu or 0128 % send email to murphy@cmu.edu 0129 0130 %icaoberg 6/1/2013 0131 answer = false; 0132 0133 % if ~isdeployed 0134 % if nargin ~= 2 0135 % error( ['CellOrganizer: Wrong number of input arguments. If slml2img ' ... 0136 % ' is not deployed, then the number of input arguments must be 2.'] ); 0137 % end 0138 % 0139 % end 0140 0141 %check if files exists and are valid SLML instances 0142 %INPUT ARGUMENTS 0143 param = varargin{2}; 0144 0145 %INPUT ARGUMENTS 0146 try 0147 verbose = param.verbose; 0148 if ~islogical( verbose ) 0149 verbose = true; 0150 end 0151 catch 0152 verbose = true; 0153 end 0154 0155 try 0156 debug = param.debug; 0157 if ~islogical( debug ) 0158 debug = false; 0159 end 0160 catch 0161 debug = false; 0162 end 0163 0164 %icaoberg 02/06/2013 0165 if ~isfield( param, 'display' ) 0166 param.display = false; 0167 end 0168 0169 %D. Sullivan 7/23/13 check for new randomwalk parameter 0170 if ~isfield(param,'randomwalk') 0171 param.randomwalk = false; 0172 end 0173 0174 %icaoberg 10/9/2012 0175 try 0176 synthesis = param.synthesis; 0177 if ~isa( synthesis, 'char' ) 0178 synthesis = 'all'; 0179 else 0180 if ~strcmpi( synthesis, 'nucleus' ) && ~strcmpi( synthesis, 'cell' ) && ... 0181 ~strcmpi( synthesis, 'framework' ) && ~strcmpi( synthesis, 'all' ) 0182 synthesis = 'all'; 0183 else 0184 synthesis = lower( synthesis ); 0185 end 0186 end 0187 catch 0188 synthesis = 'all'; 0189 end 0190 0191 % R. Arepally 6/7/13 shiftvector empty array is instantiated 0192 % so that it can be passed to im2blender. 0193 shiftvector = []; 0194 0195 %mmackie June 1st 2012 0196 %see what type of image to return, default is tif 0197 %dsullivan July 26 2012 0198 %edited from try-catch to if statement and changed from 0199 %param.image to param.output 0200 %moved to top of program, no reason to be checking this now 0201 if ~isfield(param,'output') 0202 param.output.tifimages = true; 0203 elseif ~isfield(param.output,'tifimages') && ~isfield(param.output,'indexedimage')&& ~isfield(param.output,'blenderfile') 0204 error('CellOrganizer: Unsupported output specified. Supported outputs for param.output are tifimages,indexedimage, and blenderfile. ') 0205 end 0206 0207 %LOGS 0208 try 0209 if verbose 0210 disp( 'Checking existence of log folder' ); 0211 end 0212 0213 if ~exist( [ pwd filesep 'log'], 'dir' ) 0214 if verbose 0215 disp( ['Making log directory ' pwd filesep 'log' ] ); 0216 end 0217 mkdir( 'log' ); 0218 end 0219 0220 c = clock; 0221 logfile = ''; 0222 for i=1:1:length(c) 0223 logfile = ['',logfile,num2str(c(i))]; %#ok<AGROW> 0224 end 0225 logfile = [ pwd filesep 'log' filesep logfile, '.log' ]; 0226 0227 fileID = fopen( logfile, 'w' ); 0228 catch err 0229 warning( 'CellOrganizer: Failed to create log file. Exiting program.' ) %#ok<*WNTAG> 0230 0231 %icaoberg 1/28/2013 0232 if debug 0233 getReport( err, 'extended' ); 0234 end 0235 0236 if ~isdeployed 0237 return 0238 else 0239 exit 0240 end 0241 end 0242 0243 filenames = varargin{1}; 0244 if verbose 0245 fprintf( 1, '%s', 'Checking the validity of input files'); 0246 end 0247 0248 %icaoberg 7/1/2013 0249 if isempty( filenames ) 0250 disp( 'List of models cannnot be empty. Exiting method.' ); 0251 return 0252 end 0253 0254 if ~isa( filenames, 'cell' ) 0255 disp( 'List of models must be a cell array. Exiting method.' ); 0256 return 0257 end 0258 0259 fprintf( fileID, '%s', 'Checking the validity of input files' ); 0260 for i=1:1:length(filenames) 0261 if ~isaFile( filenames{i} ) 0262 if verbose 0263 fprintf( 1, '\n%s', ['Input argument ' filenames{i} ' is not a file'] ); 0264 end 0265 0266 fprintf( fileID, '\n%s', ['Input argument ' filenames{i} ' is not a file'] ); 0267 fclose( fileID ); 0268 0269 %icaoberg 7/1/2013 0270 disp( ['Input argument ' filenames{i} ' is not a file'] ); 0271 return 0272 else 0273 n=length(filenames); 0274 %icaoberg 7/1/2013 0275 % if verbose 0276 % %indicate an object has been successfully added 0277 % fprintf( 1, [ repmat('\b', 1, length(num2str(100*(i-1)/n))+1) '%s'], ... 0278 % repmat(' ', 1, length(num2str(100*(i-1)/n))+1) ); 0279 % fprintf( 1, [ repmat('\b', 1, length(num2str(100*(i-1)/n))+1) '%s%%'], num2str(100*i/n) ); 0280 % pause(0.1) 0281 % end 0282 end 0283 end 0284 0285 % %parse SLML instances into Matlab structures 0286 % icaoberg 7/1/2013 0287 if verbose 0288 fprintf( 1, '\n%s', 'Parsing SLML instances' ); 0289 end 0290 0291 fprintf( fileID, '%s', 'Parsing SLML instances' ); 0292 try 0293 for j=1:1:length(filenames) 0294 %if it is a mat file then load directly into memory 0295 if( isMatFile(filenames{j}) ) 0296 load(filenames{j}); 0297 models{j} = model; 0298 else 0299 models{j} = slml2model( filenames{j} ); 0300 end 0301 0302 n=length(filenames); 0303 %icaoberg 7/1/2013 0304 % if verbose 0305 % %indicate an object has been successfully added 0306 % fprintf( 1, [ repmat('\b', 1, length(num2str(100*(j-1)/n))+1) '%s'], ... 0307 % repmat(' ', 1, length(num2str(100*(j-1)/n))+1) ); 0308 % fprintf( 1, [ repmat('\b', 1, length(num2str(100*(j-1)/n))+1) '%s%%'], num2str(100*j/n) ); 0309 % pause(0.1) 0310 % end 0311 end 0312 catch err 0313 warning( 'Unable to parse SLML instances. Exiting program.' ); 0314 fprintf( fileID, '%s\n', 'Unable to parse SLML instances. Exiting progam.' ); 0315 0316 %icaoberg 1/28/2013 0317 if debug 0318 getReport( err, 'extended' ); 0319 end 0320 0321 if verbose 0322 fprintf( 1, '%s\n', 'Unable to parse SLML instances. Exiting progam.' ); 0323 end 0324 0325 fprintf( fileID, '%s\n', 'Closing log file' ); 0326 fclose( fileID ); 0327 0328 if ~isdeployed 0329 return 0330 else 0331 exit 0332 end 0333 end 0334 0335 %TEMPORARY FOLDER 0336 fprintf( fileID, '\n%s\n', 'Checking existence of temporary folder' ); 0337 if verbose 0338 fprintf( 1, '\n%s\n', 'Checking existence of temporary folder' ); 0339 end 0340 0341 %icaoberg 7/30/2012 0342 if exist([pwd filesep 'temp'], 'dir' ) 0343 fprintf( fileID, '%s\n', ['Temporary folder found in ' pwd filesep 'temp. Removing all temporary files.'] ); 0344 if verbose 0345 fprintf( 1, '%s\n', ['Temporary folder found in ' pwd filesep 'temp. Removing all temporary files.'] ); 0346 end 0347 %delete([pwd filesep '*.mat']); 0348 %rmdir([pwd filesep 'temp'], 's'); 0349 %mkdir([pwd filesep 'temp']); 0350 else 0351 fprintf( fileID, '%s\n', ['Creating temporary folder in: ' pwd filesep 'temp'] ); 0352 if verbose 0353 fprintf( 1, '%s\n', ['Creating temporary folder in: ' pwd filesep 'temp'] ); 0354 end 0355 mkdir([pwd filesep 'temp']); 0356 end 0357 0358 %SETTING ARGUMENTS 0359 try 0360 targetDirectory = param.targetDirectory; 0361 catch err 0362 targetDirectory = pwd; 0363 end 0364 0365 fprintf( fileID, '%s\n', ['Setting target directory to: ' targetDirectory ] ); 0366 if verbose 0367 fprintf( 1, '%s\n', ['Setting target directory to: ' targetDirectory ] ); 0368 end 0369 0370 %setting prefix 0371 try 0372 prefix = param.prefix; 0373 catch 0374 prefix = 'demo'; 0375 end 0376 0377 fprintf( fileID, '%s\n', ['Setting prefix to: ' prefix ] ); 0378 if verbose 0379 fprintf( 1, '%s\n', ['Setting prefix to: ' prefix ] ); 0380 end 0381 0382 %setting number of synthesized images 0383 if isdeployed 0384 numberOfSynthesizedImages = str2double( varargin{3} ); 0385 else 0386 try 0387 numberOfSynthesizedImages = param.numberOfSynthesizedImages; 0388 catch err 0389 numberOfSynthesizedImages = 1; 0390 end 0391 end 0392 0393 fprintf( fileID, '%s\n', ['Setting number of synthesized images to: ' num2str(numberOfSynthesizedImages) ] ); 0394 if verbose 0395 fprintf( 1, '%s\n', ['Setting number of synthesized images to: ' num2str(numberOfSynthesizedImages) ] ); 0396 end 0397 0398 %setting compression 0399 try 0400 compression = param.compression; 0401 catch err 0402 compression = 'none'; 0403 end 0404 0405 fprintf( fileID, '%s\n', ['Setting compression to: ' compression ] ); 0406 if verbose 0407 fprintf( 1, '%s\n', ['Setting compression to: ' compression ] ); 0408 end 0409 0410 %synthesize multicolor images and save them to disk 0411 for i=1:1:numberOfSynthesizedImages 0412 if verbose 0413 disp( ['Synthesizing image ' num2str(i) '. Please wait, this might take several minutes.' ] ); 0414 end 0415 0416 fprintf( fileID, '%s\n', ['Synthesizing image ' num2str(i) '. Please wait, this might take several minutes.' ] ); 0417 0418 % try 0419 param.fileID = fileID; 0420 imgs = model2img( models, param ); 0421 0422 %mmackie June 1st 2012 0423 %see what method for determining index, default is summation 0424 %dsullivan July 26 2012 0425 %changed to param.output boolean flag structure 0426 if isfield(param.output,'indexedimage') && param.output.indexedimage 0427 mapping = 1:length(imgs); 0428 mapping(1) = 2; 0429 mapping(2) = 1; 0430 0431 %icaoberg 8/10/2012 0432 imgs = ims2index(imgs,mapping); 0433 end 0434 0435 if isempty( imgs ) 0436 disp( ['Unable to synthesize image ' ... 0437 num2str(i) ' from the given models. Continuing synthesis.'] ); 0438 continue 0439 end 0440 % catch err 0441 % %icaoberg 1/28/2013 0442 % getReport( err, 'extended' ); 0443 % 0444 % warning( 'CellOrganizer: Unable to synthesize an image from the given models. Exiting program.' ); 0445 % fprintf( fileID, '%s\n', 'Unable to synthesize an image from the given models. Exiting progam.' ); 0446 % if verbose 0447 % disp('Closing log file.') 0448 % end 0449 % 0450 % fprintf( fileID, '%s\n', 'Closing log file' ); 0451 % fclose( fileID ); 0452 % 0453 % if ~exist([pwd filesep 'temp'], 'dir' ) 0454 % rmdir([pwd filesep 'temp'],'s'); 0455 % end 0456 % 0457 % if ~isdeployed 0458 % return 0459 % else 0460 % exit 0461 % end 0462 % end 0463 0464 if strcmpi( models{1}.dimensionality, '2d' ) 0465 temporary_file = [ pwd filesep 'temp' filesep 'image.mat' ]; 0466 if exist( temporary_file ) 0467 load( temporary_file ); 0468 0469 %icaoberg 7/1/2013 0470 img2tif( imgs{1},[ targetDirectory filesep prefix num2str(i) ... 0471 '.tif'], compression ); 0472 clear img 0473 delete( temporary_file ); 0474 end 0475 0476 %mmackie June 1st 2012 0477 %dsullivan July 26 2012 0478 %changed to boolean param.output options (can turn all on at once) 0479 else 0480 outdir = [ targetDirectory filesep prefix filesep 'cell' num2str(i) ]; 0481 if ~exist( outdir, 'dir' ) 0482 mkdir ( outdir ) 0483 end 0484 0485 %if indexed image flag is true, save as indexed image 0486 if isfield(param.output,'indexedimage') && param.output.indexedimage 0487 if verbose 0488 disp( 'Saving indexed image' ); 0489 end 0490 0491 fprintf( fileID, '%s\n', 'Saving indexed image' ); 0492 img2tif( imgs, [ outdir filesep 'indexed.tif'], compression, true) ; 0493 end 0494 0495 %icaoberg 10/9/2012 0496 if strcmpi( synthesis, 'nucleus' ) || strcmpi( synthesis, ... 0497 'framework' ) || strcmpi( synthesis, 'all' ) 0498 load( [ pwd filesep 'temp' filesep 'image1.mat' ] ); 0499 %added conditional for synthesis option 0500 if isfield(param.output,'tifimages') && param.output.tifimages 0501 if verbose 0502 disp( 'Saving nuclear channel tif image' ); 0503 end 0504 0505 fprintf( fileID, '%s\n', 'Saving nuclear channel tif image' ); 0506 img2tif( img, [ outdir filesep 'nucleus.tif'], compression ); 0507 end 0508 0509 %added conditional for synthesis option 0510 if isfield(param.output,'blenderfile')&& param.output.blenderfile 0511 %7/25/12 DPS blender files 0512 if verbose 0513 disp( 'Saving nuclear channel object file' ); 0514 end 0515 fprintf( fileID, '%s\n', 'Saving nuclear channel .obj file' ); 0516 0517 %icaoberg 8/10/2012 0518 % im2blender(img,[ outdir filesep 'nucleus.obj'], ... 0519 % param.output.blender.downsample ) 0520 % Rohan Arepally 6/7/13 added [] and shiftvector to parameters 0521 % also shiftvector is returned by the function im2blender. 0522 [shiftvector, ~] = im2blender(img,[ outdir filesep 'nucleus.obj'],param.output.blender.downsample, ... 0523 [],shiftvector); 0524 end 0525 if isfield(param.output,'SBML')&¶m.output.SBML 0526 % framework2SBML('nucleus',imgs{1},'cell.xml',[]); 0527 end 0528 clear image; 0529 end 0530 0531 %cell membrane 0532 if strcmpi( synthesis, 'cell' ) || strcmpi( synthesis, ... 0533 'framework' ) || strcmpi( synthesis, 'all' ) 0534 load( [ pwd filesep 'temp' filesep 'image2.mat' ] ); 0535 if isfield(param.output,'tifimages') && param.output.tifimages 0536 if verbose 0537 disp( 'Saving cell channel tif image' ); 0538 end 0539 0540 fprintf( fileID, '%s\n', 'Saving cell channel tif image' ); 0541 0542 img2tif( img, [ outdir filesep 'cell.tif'], compression ); 0543 end 0544 0545 %7/25/12 DPS blender files 0546 if isfield(param.output,'blenderfile') && param.output.blenderfile 0547 if verbose 0548 disp( 'Saving cell channel .obj file' ); 0549 end 0550 fprintf( fileID, '%s\n', 'Saving cell channel .obj file' ); 0551 0552 %icaoberg 8/10/2012 0553 % im2blender(img,[ outdir filesep 'cell.obj'],param.output.blender.downsample) 0554 % Rohan Arepally 6/7/13 added [] and shiftvector to parameters 0555 % also shiftvector is returned by the function im2blender. 0556 im2blender(img,[ outdir filesep 'cell.obj'], ... 0557 param.output.blender.downsample , [], shiftvector); 0558 end 0559 if isfield(param.output,'SBML')&¶m.output.SBML 0560 % framework2SBML('cell',imgs{2},'cell.xml',[]); 0561 end 0562 0563 clear image; 0564 end 0565 0566 %icaoberg 10/9/2012 0567 %will only perform this tasks if synthesis is set to all 0568 if strcmpi( synthesis, 'all' ) 0569 %create framework struct for SBML model using the first two 0570 %images (nuc, cell) 0571 if (isfield(param.output,'SBML')&¶m.output.SBML) 0572 frameworkSBML = createSBMLFrameworkstruct(imgs(1:2)) 0573 end 0574 for j=1:1:length(models) 0575 if ~strcmpi( models{j}.proteinShape.class, 'centrosome' ) 0576 load( [ pwd filesep 'temp' filesep 'image' num2str(j+2) '.mat' ] ) 0577 if isfield(param.output,'tifimages') && param.output.tifimages 0578 if verbose 0579 disp( ['Saving protein channel image ' models{j}.proteinShape.class ] ); 0580 end 0581 fprintf( fileID, '%s\n', ['Saving protein channel image ' models{j}.proteinShape.class] ); 0582 0583 img2tif( img, [ outdir filesep models{j}.proteinShape.class '.tif'], compression ); 0584 end 0585 %7/25/12 DPS blender files 0586 if isfield(param.output,'blenderfile') && param.output.blenderfile 0587 if verbose 0588 disp( ['Saving protein channel object file ' models{j}.proteinShape.class ] ); 0589 end 0590 % R. Arepally 6/7/13 added [] and shiftvector as 0591 % parameters to im2blender. 0592 im2blender(img,[ outdir filesep models{j}.proteinShape.class '.obj'],param.output.blender.downsample ... 0593 ,[], shiftvector); 0594 % im2blender(img,[ outdir filesep models{j}.proteinShape.class '.obj'],param.output.blender.downsample) 0595 end 0596 %7/25/12 DPS end addition 0597 %D. Sullivan 7/23/13 added primitives type of output 0598 if (isfield(param.output,'SBML')&¶m.output.SBML) 0599 % savedatfile([outdir filesep models{j}.proteinShape.class filesep models{j}.proteinShape.class],models{j}.proteinShape.resolution,param.output.blender.downsample); 0600 primitives = createSBMLstruct(models{j}.proteinShape,num2str(j)); 0601 if isfield(param.output.SBML,'primitives')&¶m.output.primitives ==1 0602 primitives.primitiveOnly = 1; 0603 end 0604 instance2SBML(primitives,frameworkSBML,'TfR.xml') 0605 % perobjmdl([outdir filesep models{j}.proteinShape.class filesep],models{j}.proteinShape.resolution); 0606 end 0607 end 0608 end 0609 end 0610 0611 end 0612 0613 %icaoberg 7/1/2013 0614 %if we got here at least one image was succesfully synthesized 0615 answer = true; 0616 end 0617 0618 %icaoberg 6/1/2013 0619 if debug 0620 save( [ pwd filesep 'temp' filesep 'param.mat' ], 'param' ); 0621 end 0622 0623 if debug 0624 save( [ pwd filesep 'temp' filesep 'param.mat' ], 'param' ); 0625 end 0626 0627 if ~debug 0628 fprintf( fileID, '%s\n', 'Removing temporary folder' ); 0629 if verbose 0630 fprintf( 1, '%s\n', 'Removing temporary files' ); 0631 delete( [ pwd filesep 'temp' filesep 'image*.mat'] ); 0632 rmdir( [ pwd filesep 'temp'], 's' ); 0633 end 0634 end 0635 0636 if verbose 0637 disp('Closing log file.') 0638 end 0639 0640 fprintf( fileID, '%s\n', 'Closing log file' ); 0641 fclose( fileID ); 0642 0643 %icaoberg 7/1/2013 0644 disp( 'Finished synthesis' );