cellorganizer v2.9.1

demos/3D/demo3D61/comparemodels.m

@@ -0,0 +1,3 @@
+options = struct('verbose',true,'includenuclear',true, ...
+    'includecell',true,'includeprot',true,'hd_threshold',10);
+slml2report('images1to5/model.mat','images11to15/model.mat',options);

demos/3D/demo3D61/demo3D61.m

@@ -59,6 +59,8 @@
     options.labels{length(options.labels)+1} = 'LAMP2';
     options.masks{i} = [directory filesep 'LAM_cell' num2str(i) '_mask_t1.tif'];
 end
+disp(dna_paths)
+pause
 
 %set the dimensionality
 dimensionality = '3D';

img2shapespace.m

@@ -0,0 +1,178 @@
+function answer = img2shapespace(varargin)
+% img2shapespace.m
+%
+% Train 3D generative SPHARM-RPDM cell shape model and creates a report
+% using the trained model.
+%
+% Input
+% -----
+% * a directory of raw or synthetic cell shape images (cell shapes file
+%       format 'LAM_cell[1-9]_ch1_t1.tif') or OME.TIFFs
+% * an options structure to override default options
+%       see http://www.cellorganizer.org/docs/2.9.0/chapters/cellorganizer_options.html#img2slml
+%       important options include
+%       .model.name for name of the model itself
+%       .model.filename for name of the file in which to store the model
+%       .model.resolution for setting image/model pixel size
+%       .downsampling for setting downsampling before model building
+%       .shape_evolution for setting whether report includes example
+%           shape evolution
+%
+% Output
+% ------
+% * a valid SLML model file
+% * a report with an embedded shape space
+
+% Soham Chakraborti (sohamc@andrew.cmu.edu)
+% R.F. Murphy (murphy@cmu.edu)
+%
+% Copyright (C) 2020 Murphy Lab
+% Computational Biology Department
+% School of Computer Science
+% 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.cbd.cmu.edu or
+% send email to murphy@cmu.edu
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+if isdeployed()
+    %when method is deployed
+    if length(varargin) == 1
+        text_file = varargin{1};
+    else
+        error('Deployed function takes only 1 argument. Exiting method.');
+        return
+    end
+
+    [filepath, name, ext] = fileparts(text_file);
+
+    if ~exist(text_file, 'file')
+        warning('Input file does not exist. Exiting method.');
+        return
+    end
+
+    disp(['Attempting to read input file ' text_file]);
+    fid = fopen(text_file, 'r' );
+
+    disp('Evaluating lines from input file');
+    while ~feof(fid)
+        line = fgets(fid);
+        disp(line);
+        try
+            eval(line);
+        catch err
+            disp('Unable to parse line');
+            getReport(err)
+            return
+        end
+    end
+    fclose(fid);
+
+    if ~exist('options', 'var')
+        options = {};
+    end
+else
+    if nargin == 2
+        dnaImagesDirectoryPath = varargin{1};
+        cellImagesDirectoryPath = varargin{2};
+        options = struct([]);
+    else
+        dnaImagesDirectoryPath = varargin{1};
+        cellImagesDirectoryPath = varargin{2};
+        options = varargin{3};
+    end
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% img2slml %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+defaultoptions = struct();
+defaultoptions.verbose = false;
+defaultoptions.debug = false;
+defaultoptions.display = false;
+defaultoptions.model.id = uuidgen();
+%is this needed?  what does it do?
+defaultoptions.train = struct( 'flag', 'cell' );
+defaultoptions.cell.class = 'cell_membrane';
+defaultoptions.cell.type = 'spharm_rpdm';
+defaultoptions.labels = 'unique';
+
+options = ml_initparam( options, defaultoptions);
+
+if ~isfield(options,'model.filename')
+    options.model.filename = [options.model.name '.mat'];
+end    
+
+if ~isfield(options,'model.resolution')
+    disp ('No resolution specified for the input images;')
+    disp ('Using default of [0.1, 0.1, 0.1]');
+    % this is the resolution of the input image
+    options.model.resolution = [0.1, 0.1, 0.1];
+end
+
+if ~isfield(options,'downsampling')
+    disp ('No downsampling specified prior to model creation;')
+    disp ('Using default of no downsampling');
+    options.downsampling = [1, 1, 1];
+end
+
+% postprocess of parameterization: alignment
+options.model.spharm_rpdm.postprocess = ~false;
+% alignment method: 'major_axis' or 'foe'
+options.model.spharm_rpdm.alignment_method = 'major_axis';
+% plane of rotation: 'xy', 'xz', 'yz' or 'xyz'
+options.model.spharm_rpdm.rotation_plane = 'xy';
+
+% degree of the descriptor
+options.model.spharm_rpdm.maxDeg = 31;
+
+% latent dimension for the model
+options.model.spharm_rpdm.latent_dim = 15;
+options.model.spharm_rpdm.segmindnaImagesDirectoryPathfraction = 0.1;
+
+if exist(dnaImagesDirectoryPath,'var') && ~isempty(dnaImagesDirectoryPath)
+    options.model.name = 'SPHARM-RPDM-NucCellShapeModel';
+    options.dnaImagesDirectoryPathleus.class = 'nuc_membrane';
+    options.dnaImagesDirectoryPathleus.type = 'spharm_rpdm';
+    options.model.spharm_rpdm.components = {'nuc', 'cell'};
+else
+    options.model.spharm_rpdm.components = {'cell'};
+    options.model.name = 'SPHARM-RPDM-CellShapeModel';
+end
+
+tic; answer = img2slml( '3D', dnaImagesDirectoryPath, ...
+    cellImagesDirectoryPath, [], options ); toc,
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+if exist( [pwd filesep options.model.filename] )
+    answer = slml2info( {[pwd filesep options.model.filename]}, options );
+
+    if exist( ['./' options.model.name '-report'])
+        rmdir(['./' options.model.name '-report'],'s')
+    end
+
+    try
+        movefile( './report' , ['./' options.model.name '-report']);
+        web(['./' options.model.name '-report' filesep 'index.html'])
+    catch
+        disp('Couldn''t rename report folder and open report in browser');
+    end
+else
+    disp ('Failed to find the model file. Exiting application.' );
+    answer = false;
+end
+end%img2shapespace