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slml2img.m
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function answer = slml2img( varargin )
% SLML2IMG Synthesizes an image from a list of SLML models.
%
% Instances may be saved in the following forms:
% a) tiff stacks: a 3D tiff image stack for each pattern generated using the input models
% b) indexed images: a single 3D tiff image stack where each pattern is represented by a number 1-n
% c) object mesh: a .obj mesh file for each pattern generated using the input models (blenderfile option)
% d) SBML-Spatial file: a Systems Biology Markup Language (SBML) instance XML file utilizing the Spatial extension in level 3 version 1
%
% List Of Input Arguments Descriptions
% ----------------------- ------------
% models A cell array of filenames
% options A structure holding the function options
%
% The shape of options 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'
% microscope (optional) Microscope model from which we select a point spread function. Default is 'none'
% synthesis (optional) Synthesis parameter that allows to
% synthesize 'nucleus', 'cell', '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', 'sampled' or 'trimmed'. 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.
% 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.
% oobthresh (optional) The proportion of a synthesized object that is permitted to fall outside the cell before the object is discarded. Default is 0.
% oobbuffer (optional) The thickness in microns of an additional buffer zone inside the boundary of a cell in which an object cannot be placed. Default is 0.
% 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
% synthesis.diffeomorphic.maximum_iterations (optional) Integer defining the maximum number of iterations during diffeo inference. Default is 100.
%
% Random walk options
% -------------------
% 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'.
%
% Helper options
% --------------
%
% debug (optional) Keeps temporary results and catches
% errors with full reports. Default is false;
% display (optional) Will make pretty plots. Turning this
% flag on will slow down synthesis. Default is
% false.
% verbose (optional) Print the intermediate steps to screen. Default is false.
%
% Outputs
% -------
% output.tifimages (optional) Boolean flag specifying whether to write out tif images. Default is true.
% output.indexedimage (optional) Boolean flag specifying whether to write out indexed image. Default is false.
% output.blenderfile (optional) Boolean flag specifying whether to write out (.obj) files for use in blender. Default is false.
% output.meshes (optional) Boolean flag specifying whether to write out (.obj) files of analytic meshes (if available, does not work with every model type). Default is false.
% output.shape_space_coords (optional) Boolean flag specifying whether to write out (.mat, .txt) files containing shape space coordinates (currently only for SPHARM geometry). Default is false.
% 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 2 representations of geometries. Default is false.
% output.SBMLDownsampling (optional) downsampling fraction for the creation of SBML Spatial files when output.SBML or output.SBMLSpatial are true (1 means no downsampling, 1/5 means 1/5 the size).
% output.SBMLSpatial (optional) boolean flag specifying whether to write out (.xml) file with SBML-Spatial 3 representations of geometries. Default is false.
% output.SBMLSpatialImage (optional) boolean flag specifying whether SBML-Spatial 3 output represents geometries with image volumes instead of meshes. Meshes are not supported by Virtual Cell. Default is false.
% output.SBMLSpatialUseCompression (optional) boolean flag specifying whether to write SBML Spatial output using compression. Default is true.
% output.SBMLSpatialUseAnalyticMeshes (optional) boolean flag specifying whether to use analytic meshes instead of isosurfaces of rasterized shapes. Default is false.
% output.SBMLSpatialVCellCompatible (optional) boolean flag specifying whether to write SBML Spatial output compatible with Virtual Cell but not the Level 3 Version 1 Release 0.90 draft specifications. Default is false.
% output.SBMLSpatialImageDownsampling (optional) downsampling fraction for the creation of SBML Spatial files when output.SBMLSpatialImage is true (1 means no downsampling, 1/5 means 1/5 the size).
% output.SBMLTranslations (optional) N x 2 cell array of strings (first column) to be replaced by other strings (second column) in CellOrganizer-generated SBML.
% output.SBMLIncludeEC (optional) boolean flag specifying whether to include an extracellular region in SBML Spatial output. Default is false.
% output.SBMLECScale (optional) scaling for extracellular region in SBML Spatial output. Default is 1.
% output.VCML.writeVCML (optional) boolean flag specifying whether to write out VCML files for use with Virtual Cell. Default is false.
% output.VCML.input_filename (optional) string specifying Virtual Cell VCML file with biochemistry which will be combined with generated geometry in output file. Default is empty string.
% output.VCML.downsampling (optional) downsampling fraction for the creation of object files (1 means no downsampling, 1/5 means 1/5 the size). Default is 1.
% output.VCML.addTranslocationIntermediates (optional) boolean flag specifying whether to create intermediate species and reactions for reactions involving non-adjacent translocations, which are valid in cBNGL but not Virtual Cell. Default is true.
% output.VCML.numSimulations (optional) number of simulations in VCML file.
% output.VCML.translations (optional) N x 2 cell array of strings (first column) to be replaced by other strings (second column).
% output.VCML.defaultDiffusionCoefficient (optional) double specifying diffusion coefficient in meters squared per second. Default is 1.0958e-11.
% output.VCML.NET.filename (optional) string specifying BioNetGen network file to include in VCML files for use with Virtual Cell. Default is empty string.
% output.VCML.NET.units.concentration (optional) string specifying concentration units in NET file. Default is 'uM'.
% output.VCML.NET.units.length (optional) string specifying length units in NET file. Default is 'um'.
% output.VCML.NET.units.time (optional) string specifying time units in NET file. Default is 's'.
% output.VCML.NET.effectiveWidth (optional) double specifying surface thickness in meters. Default is 3.8775e-9.
% output.VCML.NET.useImageAdjacency (optional) boolean specifying whether to derive compartment adjacency from the synthetic image. Can break Virtual Cell compatibility due to inclusion of BioNetGen representation of translocation between non-adjacent compartments. Default is true.
% output.MCellMDL.writeMCellMDL (optional) boolean flag specifying whether to write out MCellMDL files for use with Virtual Cell. Default is false.
% output.MCellMDL.downsampling (optional) downsampling fraction for the creation of object files (1 means no downsampling, 1/5 means 1/5 the size). Default is 1.
% output.MCellMDL.addTranslocationIntermediates (optional) boolean flag specifying whether to create intermediate species and reactions for reactions involving non-adjacent translocations, which are valid in cBNGL but not Virtual Cell. Default is true.
% output.MCellMDL.numSimulations (optional) number of simulations in MCellMDL file.
% output.MCellMDL.translations (optional) N x 2 cell array of strings (first column) to be replaced by other strings (second column).
% output.MCellMDL.defaultDiffusionCoefficient (optional) double specifying diffusion coefficient in meters squared per second. Default is 1.0958e-11.
% output.MCellMDL.input_filename_pattern (optional) string specifying pattern matching a set of MCell MDL files to be combined with generated MDL files. This should be empty or `[path][prefix].*.[extension]`. Extension can be `.mdl`, `.mcell`, or otherwise. If not empty, CellOrganizer will only generate the geometry file and will copy the other files matching the pattern to the output directory, and it is the user's responsibility to ensure compatibility between the input and CellOrganizer's output. Default is `''`. Only one of `output.MCellMDL.input_filename_pattern` and `output.NET.filename` can be non-empty.
% output.NET.filename (optional) string specifying BioNetGen network file to include in VCML or MCell MDL files for use with Virtual Cell or MCell MDL files for MCell. Default is `''`. Only one of `output.MCellMDL.input_filename_pattern` and `output.NET.filename` can be non-empty.
% output.NET.units.concentration (optional) string specifying concentration units in NET file. Default is 'uM'.
% output.NET.units.length (optional) string specifying length units in NET file. Default is 'um'.
% output.NET.units.time (optional) string specifying time units in NET file. Default is 's'.
% output.NET.effectiveWidth (optional) double specifying surface thickness in meters. Default is 3.8775e-9.
% output.NET.useImageAdjacency (optional) boolean specifying whether to derive compartment adjacency from the synthetic image. Can break Virtual Cell compatibility due to inclusion of BioNetGen representation of translocation between non-adjacent compartments. Default is true.
% output.OMETIFF (optional) boolean flag specifying whether to write out an (.ome.tif) OME TIFF. Default is false.
%
% PCA model options
% ------------------
% model.pca.pca_synthesis_method (mandatory)['reconstruction' or 'random sampling']
% model.pca.imageSize (mandatory)
%
%3D SPHARM-RPDM model options
% ------------------
%model.spharm_rpdm.synthesis_method ['reconstruction' or 'random sampling']
%
%
%T cell distribution model options
% ------------------
% model.tcell.results_location (mandatory)File path for where the results should be saved.
% model.tcell.named_option_set (mandatory)The running choice for CellOrganizer and one sensor of two-point annotation
% model.tcell.use_two_point_synapses (optional)Set up the mode of synapse to use, as a default, we use one-point,
% if needed you can use two-point by set up the option as true
% model.tcell.sensor (mandatory)Set up protein name
% model.tcell.timepoints_to_include (optional)If creation of models for only a subset of the time points is desired,
% edit to specify which time points to include
% model.tcell.model_type_to_include (mandatory)Set up for model to include
% Example
% -------
% instances = { 'model01.xml', 'model02.mat', 'model03.mat' };
% options.targetDirectory = pwd;
% options.prefix = 'demo'
% options.numberOfSynthesizedImages = 100;
% options.compression = 'lzw';
% options.microscope = 'svi';
% options.verbose = true;
%
% >> slml2img( instances, options );
% Ivan E. Cao-Berg ([email protected])
%
% Copyright (C) 2007-2018 Murphy Lab
% Computational Biology Department
% Carnegie Mellon University
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published
% by the Free Software Foundation; either version 2 of the License,
% or (at your option) any later version.
%
% This program is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
% 02110-1301, USA.
%
% For additional information visit http://murphylab.web.cmu.edu or
% send email to [email protected]
% March 7, 2012 R.F.Murphy Don't create directory to hold 3D images if
% generating 2D
%
% March 8, 2012 I. Cao-Berg Documented the method
%
% March 9, 2012 I. Cao-Berg Changed disp to fprintf and improved logs
%
% March 9, 2012 I. Cao-Berg Removed print of progress bar from log file
%
% March 21, 2012 I. Cao-Berg Changed protein.location to protein.cytonuclearflag
%
% April 11, 2012 I. Cao-Berg Removed removal of temporary folder
%
% June 5, 2012 M. Mackie Added option to save as an index image using
% options.image.type and options.image.option
%
% June 6, 2012 M. Mackie Removed parameter image.option (index images
% may only be saved as 'priority'
%
% July 25, 2012 D. Sullivan Added fields options.blender.file and options.blender.downsample
% Created option for saving .obj files for exporting to blender
%
% July 26, 2012 D. Sullivan Changed options.image and options.blender structures
% to options.output structure (see header for usage)
%
% July 30, 2012 I. Cao-Berg Modified code that is res files in the temporary folder rather than
% the folder itself. This way if a user trains a model and synthesizes
% images in the same script, the temp folder remains intact in case it is
% run in debug mode
%
% August 20, 2012 I. Cao-Berg Renamed img2blender to im2blender
%
% October 1, 2012 I. Cao-Berg Removed deprecated code from previous versions
%
% October 9, 2012 I. Cao-Berg Added print of the error stack if method
% fails to synthesize an image
%
%January 28, 2012 I. Cao-Berg Updated try/catch statement to print an
% error report when running debug mode
%
% April 29, 2013 D. Sullivan added documentation for options.debug
%
% May 18, 2013 I . Cao-Berg Updated method so if framework fails to
% synthesize it returns an empty framework
%
% June 7, 2013 R. Arepally added the variable shiftvector as a parameter to
% the im2blender function. This fixes the bug of inconsistant shifting of
% different objects when the blender files are created.
%
% July 23, 2013 D. Sullivan added primitives type of output
%
% January 25, 2016 I. Cao-Berg Fixed bug where method was overwritting
% existing frameworks and appending protein patterns
%
% April 4, 2016 I. Cao-Berg Updated method to reflect the refactoring
%
% November 10, 2016 I. Cao-Berg Added support for SBML Spatial 3
%
% November 15, 2016 I. Cao-Berg Added support for OME.TIFF
%
% November 28, 2016 I. Cao-Berg Included new option that allows users to overwrite synthetic images
%
% January 25, 2017 I. Cao-Berg Fixed issue with the code where call to SBML
% Spatial fails if output flag is missing
%
% January 13, 2018 I. Cao-Berg Cleaned up method
%
% February 20, 2018 I. Cao-Berg Updated method to save 2D images as OMETIFF
%icaoberg 6/1/2013
answer = false;
if parallel.gpu.GPUDevice.isAvailable
disp('GPU Device available. Will attempt to use to speed computation.');
end
if isdeployed
filename = is_deployed(varargin{1});
load(filename);
else
if length(varargin) >= 1
filenames = varargin{1};
options = varargin{2};
else
warning('At least one argument must be provided. Exiting method');
return;
end
end
options = get_cellorganizer_default_parameters( 'synthesis', options );
%icaoberg 10/9/2012
synthesis = options.synthesis;
disp('Setting synthesis option');
if ~strcmpi( synthesis, 'nucleus' ) && ~strcmpi( synthesis, 'cell' ) && ...
~strcmpi( synthesis, 'framework' ) && ~strcmpi( synthesis, 'all' )
disp('Unknown synthesis option. Setting synthesis option to '' all ''');
synthesis = 'all';
else
synthesis = lower( synthesis );
end
% R. Arepally 6/7/13 shiftvector empty array is instantiated
% so that it can be passed to im2blender.
shiftvector = [];
%mmackie June 1st 2012
%see what type of image to return, default is tif
%dsullivan July 26 2012
%edited from try-catch to if statement and changed from
%options.image to options.output
%moved to top of program, no reason to be checking this now
%D. Sullivan 12/4/14 - updated supported outputs
if ~isfield(options,'output')
options.output.tifimages = true;
elseif ~isfield(options.output,'tifimages') && ...
~isfield(options.output,'indexedimage')&& ...
~isfield(options.output,'blenderfile') && ...
~isfield(options.output,'meshes') && ...
~isfield(options.output,'SBML') && ...
~isfield(options.output,'SBMLSpatial') && ...
~options.output.VCML.writeVCML && ...
~options.output.MCellMDL.writeMCellMDL
error(['CellOrganizer: Unsupported output specified. Supported ' ...
'outputs for options.output are tifimages, indexedimage, SBML, SBMLSpatial, VCML, and MCellMDL.'])
end
%LOGS
try
if options.verbose
disp( 'Checking existence of log folder' );
end
if ~exist( [ pwd filesep 'log'], 'dir' )
if options.verbose
disp( ['Making log directory ' pwd filesep 'log' ] );
end
mkdir( 'log' );
end
% c = clock;
% logfile = '';
% for i=1:1:length(c)
% logfile = ['',logfile,num2str(c(i))]; %#ok<AGROW>
% end
logfile = datestr(datetime('now', 'TimeZone', 'local'), 'yyyymmddHHMMSS.FFF'); %#ok<AGROW>
logfile = [ pwd filesep 'log' filesep logfile, '.log' ];
fileID = fopen( logfile, 'w' );
catch err
warning( 'CellOrganizer: Failed to create log file. Exiting program.' ) %#ok<*WNTAG>
%icaoberg 3/5/2015
getReport( err, 'extended' )
end
if options.verbose
fprintf( 1, '%s', 'Checking the validity of input files');
end
%icaoberg 7/1/2013
if isempty( filenames )
disp( 'List of models cannnot be empty. Exiting method.' );
return
end
if ~isa( filenames, 'cell' )
disp( 'List of models must be a cell array. Exiting method.' );
return
end
fprintf( fileID, '%s', 'Checking the validity of input files' );
for i=1:1:length(filenames)
if ~isaFile( filenames{i} )
if options.verbose
fprintf( 1, '\n%s', ['Input argument ' filenames{i} ' is not a file'] );
end
fprintf( fileID, '\n%s', ['Input argument ' filenames{i} ' is not a file'] );
fclose( fileID );
%icaoberg 7/1/2013
disp( ['Input argument ' filenames{i} ' is not a file'] );
return
else
n=length(filenames);
end
end
% %parse SLML instances into Matlab structures
% icaoberg 7/1/2013
if options.verbose
fprintf( 1, '\n%s', 'Parsing SLML instances' );
end
fprintf( fileID, '%s', 'Parsing SLML instances' );
try
for j=1:1:length(filenames)
%if it is a mat file then load directly into memory
if( isMatFile(filenames{j}) )
load(filenames{j});
models{j} = model;
else
models{j} = slml2model( filenames{j} );
end
n = length(filenames);
end
catch err
warning( 'Unable to parse SLML instances. Exiting program.' );
fprintf( fileID, '%s\n', 'Unable to parse SLML instances. Exiting progam.' );
%icaoberg
if options.debug
getReport( err, 'extended' )
end
if options.verbose
fprintf( 1, '%s\n', 'Unable to parse SLML instances. Exiting progam.' );
end
fprintf( fileID, '%s\n', 'Closing log file' );
fclose( fileID );
if ~isdeployed
return
else
exit
end
end
if isempty( models )
warning( 'No model able to be loaded from filenames provided. Exiting method' );
return;
end
%TEMPORARY FOLDER
disp( 'Checking existence of temporary folder' );
%icaoberg 7/30/2012
if exist(options.temporary_results, 'dir' )
disp(['Temporary folder found in ' options.temporary_results '. Removing all temporary files.'] );
%removes temp image files and temp results related to microtubules
clean_synthesis_temp_files();
else
disp( ['Creating temporary folder in ' options.temporary_results ]);
mkdir(options.temporary_results);
end
%SETTING ARGUMENTS
%setting target directory
targetDirectory = options.targetDirectory;
if isempty( targetDirectory )
targetDirectory = pwd;
end
disp( ['Setting target directory to ' targetDirectory ] );
%icaoberg 12/2/2013
if ~exist( targetDirectory, 'dir' )
disp( 'Target directory does not exist. Making target directory.' );
mkdir( targetDirectory )
end
%setting prefix
prefix = options.prefix;
fprintf( fileID, '%s\n', ['Setting prefix to: ' prefix ] );
if options.verbose
fprintf( 1, '%s\n', ['Setting prefix to: ' prefix ] );
end
%setting number of synthesized images
numberOfSynthesizedImages = options.numberOfSynthesizedImages;
disp( ['Setting number of synthesized images to ' num2str(numberOfSynthesizedImages) ] );
%setting compression
compression = options.compression;
disp( ['Setting compression to ' compression ] );
try
dimensionality = models{1}.dimensionality;
catch
warning('Unable to set model dimensionality');
end
disp('Checking all models have the same dimensionality');
for i=1:1:length(models)
if ~strcmpi( models{i}.dimensionality, dimensionality )
disp('Models have different dimensionality. Unable to synthesize image. Exiting method.');
if ~isempty( fileID )
fprintf( fileID, '%s\n', 'Models have different dimensionality. Unable to synthesize image.' );
end
return;
end
end
if strcmpi(dimensionality, '3D')
maxres = inf(1,3);
elseif strcmpi(dimensionality, '2D')
maxres = inf(1,2);
else
error('CellOrganizer: unsupported dimensionality')
end
% Prevent later changes to resolution that seem to depend on resampling that only occurs for synthesis == 'all'
if any(strcmpi(synthesis, {'cell', 'nucleus', 'framework'}))
for i = 1:length(models)
if isfield(models{i}, 'proteinModel')
models{i} = rmfield(models{i}, 'proteinModel');
end
end
end
%setting protein resolution
disp( 'Setting protein model resolution')
for i = 1:length(models)
if isfield(models{i}, 'proteinModel')
maxres = min(models{i}.proteinModel.resolution,maxres);
elseif isfield(models{i},'cellShapeModel')
maxres = min(models{i}.cellShapeModel.resolution,maxres);
elseif isfield(models{i},'nuclearShapeModel')
maxres = min(models{i}.nuclearShapeModel.resolution,maxres);
end
end
%icaoberg 11/5/2014
if isfield( options, 'resolution' )
options.resolution = ml_initparam(options.resolution,struct('objects',maxres));
else
options.resolution.objects = maxres;
end
disp(['Protein model object(s) resolution set to ' mat2str(options.resolution.objects) ]);
options.resolution.cubic = ...
repmat(min(options.resolution.objects),...
size(options.resolution.objects,1),size(options.resolution.objects,2));
%synthesize multicolor images and save them to disk
for i=1:1:numberOfSynthesizedImages
if ~options.overwrite_synthetic_instances
if exist([options.targetDirectory filesep options.prefix filesep 'cell' num2str(i)], 'dir')
continue
end
else
temporary_target_directory = ...
[options.targetDirectory filesep options.prefix filesep 'cell' num2str(i)];
if exist( temporary_target_directory, 'dir' ) && options.clean_synthetic_instances
rmdir(temporary_target_directory, ...
's' );
mkdir(temporary_target_directory);
end
end
if options.verbose
disp( ['Synthesizing image ' num2str(i) '. Please wait, this might take several minutes.' ] );
end
options.fileID = fileID;
%D. Sullivan 2/24/14
[imgs,options] = model2img( models, options );
if isempty( imgs )
disp( ['Unable to synthesize image ' ...
num2str(i) ' from the given models. Continuing synthesis.'] );
continue
end
%mmackie June 1st 2012
%see what method for determining index, default is summation
%dsullivan July 26 2012
%changed to options.output boolean flag structure
if field_exists_and_true(options.output,'indexedimage')
mapping = 1:length(imgs);
if strcmpi( synthesis, 'framework' ) || strcmpi( synthesis, 'all' )
mapping(1) = 2;
mapping(2) = 1;
end
%icaoberg 8/10/2012
indexed_image = ims2index(imgs,mapping);
end
if isempty( imgs )
disp( ['Unable to synthesize image ' ...
num2str(i) ' from the given models. Continuing synthesis.'] );
continue
end
if strcmpi( models{1}.dimensionality, '2d' )
temporary_file = [ options.temporary_results filesep 'image.mat' ];
if options.output.tifimages
if exist( temporary_file, 'file' )
load( temporary_file );
outdir = [ targetDirectory filesep prefix filesep 'cell' num2str(i) ];
if ~exist( outdir, 'dir' )
mkdir ( outdir )
end
img2tif( imgs{1},[ outdir filesep 'cell' num2str(i) ...
'.tif'], compression );
clear img
end
end
if options.output.OMETIFF
if exist( temporary_file, 'file' )
load( temporary_file );
outdir = [ targetDirectory filesep prefix filesep 'cell' num2str(i) ];
if ~exist( outdir, 'dir' )
mkdir ( outdir )
end
temporary_file = [options.temporary_results filesep 'image.mat'];
temporary_image = load( temporary_file );
temporary_image = temporary_image.imgs{1};
list_of_input_images = {};
list_of_channel_labels = {};
for index=1:1:size(temporary_image, 3)
list_of_input_images{index} = [options.temporary_results filesep 'channel' num2str(index) '.tif' ];
img2tif( temporary_image(:,:,index), list_of_input_images{index}, 'lzw' );
list_of_channel_labels{index} = ['channel' num2str(index)];
end
output_filename = [outdir filesep ...
'cell' num2str(i) '.ome.tif'];
parameters.PhysicalSizeX = options.resolution.objects(1);
parameters.PhysicalSizeY = options.resolution.objects(2);
parameters.list_of_channel_labels = list_of_channel_labels;
answer = tif2ometiff( list_of_input_images, output_filename, parameters );
clear temporary_image list_of_channel_labels;
delete([options.temporary_results filesep 'channel*.tif' ]);
end
end
if exist( temporary_file, 'file' )
delete( temporary_file );
end
else
%icaoberg 01/25/2016
%made changes to prevent overwritten existing cell image folders
index = length(dir([targetDirectory filesep prefix filesep 'cell*']))+1;
outdir = [ targetDirectory filesep prefix filesep 'cell' num2str(i) ];
if ~exist( outdir, 'dir' )
mkdir ( outdir )
end
if field_exists_and_true(options.output,'shape_space_coords')
shape_space_coords = [];
if isfieldr(options, 'spharm_rpdm.shape_space_coords')
shape_space_coords = options.spharm_rpdm.shape_space_coords;
end
if ~isempty(shape_space_coords)
save([outdir filesep 'shape_space_coords.mat'], 'shape_space_coords');
fid = fopen([outdir filesep 'shape_space_coords.txt'], 'w');
for j = 1:length(shape_space_coords)
if j > 1
fprintf(fid, ' ');
end
fprintf(fid, '%.17e', shape_space_coords(j));
end
fclose(fid);
end
end
%if indexed image flag is true, save as indexed image
if field_exists_and_true(options.output,'indexedimage')
if options.verbose
disp( 'Saving indexed image' );
end
fprintf( fileID, '%s\n', 'Saving indexed image' );
img2tif( indexed_image, [ outdir filesep 'indexed.tif'], compression, true) ;
imwrite( reshape_contrast(single(indexed_image), -1), [ outdir filesep 'indexed.png']) ;
end
resolution_cubic_to_objects = options.resolution.objects ./ options.resolution.cubic
resolution_to_um = resolution_cubic_to_objects .* options.resolution.cubic
%icaoberg 10/9/2012
if strcmpi( synthesis, 'nucleus' ) || strcmpi( synthesis, ...
'framework' ) || strcmpi( synthesis, 'all' )
load( [ options.temporary_results filesep 'image1.mat' ] );
%added conditional for synthesis option
if field_exists_and_true(options.output,'tifimages')
if options.verbose
disp( 'Saving nuclear channel tif image' );
end
fprintf( fileID, '%s\n', 'Saving nuclear channel tif image' );
img2tif( img, [ outdir filesep 'nucleus.tif'], compression );
end
%added conditional for synthesis option
if field_exists_and_true(options.output,'blenderfile')
%7/25/12 DPS blender files
if options.verbose
disp( 'Saving nuclear channel object file' );
end
fprintf( fileID, '%s\n', 'Saving nuclear channel .obj file' );
%icaoberg 8/10/2012
% im2blender(img,[ outdir filesep 'nucleus.obj'], ...
% options.output.blender.downsample )
% Rohan Arepally 6/7/13 added [] and shiftvector to parameters
% also shiftvector is returned by the function im2blender.
[shiftvector, ~] = im2blender(img,[ outdir filesep 'nucleus.obj'],options.output.blender.downsample, ...
[],shiftvector);
end
clear image;
end
%cell membrane
if strcmpi( synthesis, 'cell' ) || strcmpi( synthesis, ...
'framework' ) || strcmpi( synthesis, 'all' )
load( [ options.temporary_results filesep 'image2.mat' ] );
if field_exists_and_true(options.output,'tifimages')
if options.verbose
disp( 'Saving cell channel tif image' );
end
fprintf( fileID, '%s\n', 'Saving cell channel tif image' );
img2tif( img, [ outdir filesep 'cell.tif'], compression );
end
%7/25/12 DPS Save output as Wavefront obj. file
if field_exists_and_true(options.output,'blenderfile')
if options.verbose
disp( 'Saving cell channel as Wavefront .obj file' );
end
fprintf( fileID, '%s\n', 'Saving cell channel .obj file' );
%icaoberg 8/10/2012
% im2blender(img,[ outdir filesep 'cell.obj'],options.output.blender.downsample)
% Rohan Arepally 6/7/13 added [] and shiftvector to parameters
% also shiftvector is returned by the function im2blender.
im2blender(img,[ outdir filesep 'cell.obj'], ...
options.output.blender.downsample , [], shiftvector);
end
clear image;
end
if field_exists_and_true_or_char(options.output,'tifimages') || ...
field_exists_and_true(options.output,'meshes') || ...
field_exists_and_true_or_char(options.output,'blenderfile') || ...
field_exists_and_true_or_char(options.output,'SBML') || ...
field_exists_and_true_or_char(options.output,'SBMLSpatial') || ...
options.output.VCML.writeVCML || ...
options.output.VCML.writeMCellMDL
%create framework struct for SBML model using the first two
%images (nuc, cell)
if (field_exists_and_true_or_char(options.output,'SBML') || ...
field_exists_and_true_or_char(options.output,'SBMLSpatial') || ...
options.output.VCML.writeVCML || ...
options.output.MCellMDL.writeMCellMDL)
%D. Sullivan 11/4/14 - adjust resolutions to be cubic since
%simulating in non-cubic voxels doesn't make sense
if (field_exists_and_true(options,'cubicOverride'))
warning('Exporting non-cubic SBML voxels!')
else
for j = 1:length(imgs)
imgs{j} = AdjustResolutions(imgs{j},options.resolution.objects,options.resolution.cubic,false);
end
% xruan 05/21/2019 also adjust resolution for meshes
if isfield(options, 'nucmesh')
options.nucmesh.vertices = options.nucmesh.vertices .* repmat(resolution_cubic_to_objects, size(options.nucmesh.vertices, 1), 1);
options.nucmesh_cubic = true;
end
if isfield(options, 'cellmesh')
options.cellmesh.vertices = options.cellmesh.vertices .* repmat(resolution_cubic_to_objects, size(options.cellmesh.vertices, 1), 1);
options.cellmesh_cubic = true;
end
end
if field_exists_and_true(options.output,'meshes')
% Write meshes generated directly by the model, not isosurface like options.output.blenderfile
% Nucleus
if options.verbose
disp( 'Saving nucleus mesh .obj file' );
end
fprintf( fileID, '%s\n', 'Saving nucleus mesh .obj file' );
output_filename_root = 'nucleus';
if (isstruct(options.nucmesh) && ...
field_exists_and_true(options,'cellmesh_cubic'))
output_filename_root = [output_filename_root '_cubic'];
end
if isstruct(options.nucmesh)
output_mesh = options.nucmesh;
else
output_mesh = struct('vertices', zeros(0, 3), 'faces', zeros(0, 3, 'uint8'));
end
nucmesh_with_objects = struct('vertices', output_mesh.vertices, 'objects', struct('type', 'f', 'data', struct('vertices', output_mesh.faces)));
write_wobj(nucmesh_with_objects, [outdir filesep output_filename_root '.obj']);
% Cell
if options.verbose
disp( 'Saving cell mesh .obj file' );
end
fprintf( fileID, '%s\n', 'Saving cell mesh .obj file' );
output_filename_root = 'cell';
if (isstruct(options.cellmesh) && ...
field_exists_and_true(options,'cellmesh_cubic'))
output_filename_root = [output_filename_root '_cubic'];
end
if isstruct(options.cellmesh)
output_mesh = options.cellmesh;
else
output_mesh = struct('vertices', zeros(0, 3), 'faces', zeros(0, 3, 'uint8'));
end
cellmesh_with_objects = struct('vertices', output_mesh.vertices, 'objects', struct('type', 'f', 'data', struct('vertices', output_mesh.faces)));
write_wobj(cellmesh_with_objects, [outdir filesep output_filename_root '.obj']);
end
if field_exists_and_true_or_char(options.output,'SBML')
frameworkSBML = createSBMLFrameworkstruct(imgs(1:min(2,end)),models,options);
else
frameworkSBML = createSBMLFrameworkstruct3(imgs(1:min(2,end)),models,options);
end
if (field_exists_and_true(options,'cubicOverride'))
warning('Exporting non-cubic SBML voxels!')
else
for j = 1:length(frameworkSBML.list)
frameworkSBML.list(j).resolution = options.resolution.cubic;
end
% Scale to micron resolution here instead of in convertCSGToMesh (previously affected only callers of convertCSGToMesh, i.e., instance2SBML3_mod and instance2MCellMDL, now affects all users of frameworkSBML below this loop).
% Impacts:
% * instance2SBML_mod (not being maintained, TODO: check)
% * nameModels (not impacted; does not use frameworkSBML as it ignores meshData argument)
% * instance2SBML3_mod (not impacted; meshes not used before convertCSGToMesh call)
% * instance2VCML (not impacted; only uses frameworkSBML by passing meshData argument to readNetworkIntoGeometry, which does not use meshData resolution fields)
% * instance2MCellMDL (not impacted; meshes not used before convertCSGToMesh call)
for j = 1:length(frameworkSBML)
for k = 1:length(frameworkSBML(j).list)
single_frameworkSBML_list_item_resolution = frameworkSBML(j).list(k).resolution;
% single_frameworkSBML_list_item_resolution = resolution_before_downsampling;
if isfield(frameworkSBML(j).list(k), 'mesh')
frameworkSBML(j).list(k).mesh.vertices = frameworkSBML(j).list(k).mesh.vertices .* repmat(single_frameworkSBML_list_item_resolution, size(frameworkSBML(j).list(k).mesh.vertices, 1), 1);
end
frameworkSBML(j).list(k).resolution = [1, 1, 1];
end
end
end
dbstack, frameworkSBML % Debug
end
%D. Sullivan 4/26/14
%now set up the extracellular matrix.
if ~isfield(options,'SBML_0Name')
options.SBML_0Name = 'EC';
end
%%%I think we should do this for the framework not the primitives%%%
primitives = struct();
if field_exists_and_true(options.output,'SBMLIncludeEC')
if (field_exists_and_true_or_char(options.output,'SBML') && field_exists_and_true(options.output,'SBMLIncludeEC'))
primitives = getBox(imgs,options.SBML_0Name,options.resolution.cubic,[],options);
end
if ((field_exists_and_true_or_char(options.output,'SBMLSpatial') && field_exists_and_true(options.output,'SBMLIncludeEC')) || ...
options.output.VCML.writeVCML || ...
options.output.MCellMDL.writeMCellMDL)
primitives = getBox3(imgs,options.SBML_0Name,options.resolution.cubic,[],options);
end
end
if length(models) > 0
switch lower(synthesis)
case {'all', 'framework'}
temporary_results_offset = 2;
case {'cell', 'nucleus'}
temporary_results_offset = 1;
end
end
if strcmpi(synthesis, 'all')
for j=1:1:length(models)
if isfield(models{j}, 'proteinModel') && ~strcmpi( models{j}.proteinModel.class, 'centrosome' )
load( [ options.temporary_results filesep 'image' num2str(j+temporary_results_offset) '.mat' ] )
if field_exists_and_true(options.output,'tifimages')
if options.verbose
disp( ['Saving protein channel image ' models{j}.proteinModel.class ] );
end
fprintf( fileID, '%s\n', ['Saving protein channel image ' models{j}.proteinModel.class] );
%D. Sullivan 12/4/14 - added model index to create
%unique identifier
% img2tif( img, [ outdir filesep models{j}.proteinModel.class '.tif'], compression );
img2tif( img, [ outdir filesep models{j}.proteinModel.class num2str(j) '.tif'], compression );
end
%7/25/12 DPS blender files
if field_exists_and_true(options.output,'blenderfile')
warning('This output is deprecated. Use of options.output.SBML is recommended instead')
if options.verbose
disp( ['Saving protein channel object file ' models{j}.proteinModel.class ] );
end
% R. Arepally 6/7/13 added [] and shiftvector as
% parameters to im2blender.
%D. Sullivan 12/4/14 - added model index to create
%unique identifier
im2blender(img,[ outdir filesep models{j}.proteinModel.class num2str(j) '.obj'],options.output.blender.downsample ...
,[], shiftvector);
% im2blender(img,[ outdir filesep models{j}.proteinModel.class '.obj'],options.output.blender.downsample)
end
%7/25/12 DPS end addition
%D. Sullivan 7/23/13 added primitives type of output
if (field_exists_and_true_or_char(options.output,'SBML') || ...
field_exists_and_true_or_char(options.output,'SBMLSpatial') || ...
options.output.VCML.writeVCML || ...
options.output.MCellMDL.writeMCellMDL)
model_class = [];
if isfield(options,'SBML_PName')
model_class = [options.SBML_PName{j},num2str(j)];
end
%D. Sullivan ***Temporary - this wont work for the HTM***
if true_or_char(options.output.SBML)
primitives = createSBMLstruct(models{j}.proteinModel,num2str(j),model_class,primitives);
end
if field_exists_and_true_or_char(options.output,'SBMLSpatial') || options.output.VCML.writeVCML || options.output.MCellMDL.writeMCellMDL
primitives = createSBMLstruct3(models{j}.proteinModel,num2str(j),model_class,primitives,options);
end
if field_exists_and_true(options.output,'primitives')
primitives.primitiveOnly = 1;
end
%D. Sullivan - 4/8/14 check that whether the SBML
%flag is pointing to a file path.
save([options.temporary_results filesep 'preSBML.mat']);
if field_exists_and_true_or_char(options.output,'SBML')
instance2SBML_mod(primitives,frameworkSBML,[outdir,'.xml'],...
options.output.SBML,options.resolution.cubic,options);
end
end
end
end
end
if (field_exists_and_true_or_char(options.output,'SBML') || ...
field_exists_and_true_or_char(options.output,'SBMLSpatial') || ...
options.output.VCML.writeVCML || ...
options.output.MCellMDL.writeMCellMDL)
options = nameModels(primitives, frameworkSBML, models, imgs, options);
end
%support for SBML Spatial Level 3 Version 1.0 Draft 0.95
if field_exists_and_true_or_char(options.output,'SBMLSpatial')
if check_if_SBML_output_supported( models )
instance2SBML3_mod(primitives,frameworkSBML, ...
models,imgs,...
[outdir filesep 'cell.xml'], options.output.SBMLSpatial, ...
options);
else
warning('Cannot generate SBML Spatial file');
end
end
% Support for Virtual Cell version 7.0.0_build_11
if options.output.VCML.writeVCML
if check_if_SBML_output_supported( models )
instance2VCML(primitives, frameworkSBML, ...
models, imgs, ...
options, [outdir filesep 'cell.vcml']);
else
warning('Cannot generate VCML file');
end
end
% Support for MCell version 3.4
if options.output.MCellMDL.writeMCellMDL
if check_if_SBML_output_supported( models )
instance2MCellMDL(primitives, frameworkSBML, ...
models, imgs, ...
options, [outdir filesep 'cell.mdl']);
else
warning('Cannot generate MCellMDL file');
end
end
end
if field_exists_and_true(options.output,'OMETIFF')
list_of_input_images = {};
list_of_channel_labels = {};
files = dir( [options.temporary_results filesep 'image*.mat' ] );
for index=1:1:length(files)
file = [ options.temporary_results filesep files(index).name ];
temp = load( file );
img2tif( temp.img, [ options.temporary_results filesep ...
'image' num2str(index) '.tif' ] );
list_of_input_images{index} = [ options.temporary_results filesep ...
'image' num2str(index) '.tif' ] ;
list_of_channel_labels{index} = ['channel' num2str(index)];
clear temp
end
clear files file
output_filename = [outdir filesep ...
'cell' num2str(i) '.ome.tif'];
parameters.PhysicalSizeX = options.resolution.objects(1);
parameters.PhysicalSizeY = options.resolution.objects(2);
parameters.PhysicalSizeZ = options.resolution.objects(3);
parameters.list_of_channel_labels = list_of_channel_labels;
answer = tif2ometiff( list_of_input_images, output_filename, parameters );
end
if field_exists_and_true(options.output,'indexedimage')
list_of_input_images = {};