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set_temp_result_folders (1 call, 0.010 sec)
Generated 05-Nov-2014 07:52:30 using cpu time.
function in file /usr0/home/jenkins/workspace/cellorganizer-demo3D11-glnx64/utilities/set_temp_result_folders.m
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Parents (calling functions)

Function NameFunction TypeCalls
img2modelfunction1
Lines where the most time was spent

Line NumberCodeCallsTotal Time% TimeTime Plot
53
end
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end
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mkdir(param.compartmentdir);
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90
if ~exist(param.compartmentdir...
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89
end
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Totals  0.010 s100% 
Children (called functions)

Function NameFunction TypeCallsTotal Time% TimeTime Plot
filesepfunction150 s0%
pwdfunction10 s0%
Self time (built-ins, overhead, etc.)  0.010 s100.0%
Totals  0.010 s100% 
Code Analyzer results
No Code Analyzer messages.
Coverage results
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Total lines in function92
Non-code lines (comments, blank lines)46
Code lines (lines that can run)46
Code lines that did run46
Code lines that did not run0
Coverage (did run/can run)100.00 %
Function listing
   time   calls  line
1 function param = set_temp_result_folders(param)
2 %SET_TEMP_RESULT_FOLDERS checks the param struct for user defined temp directories, if not
3 %specified defaults them
4 %
5 %Author: Devin Sullivan 6/13/13
6 %
7 % This program is free software; you can redistribute it and/or modify
8 % it under the terms of the GNU General Public License as published
9 % by the Free Software Foundation; either version 2 of the License,
10 % or (at your option) any later version.
11 %
12 % This program is distributed in the hope that it will be useful, but
13 % WITHOUT ANY WARRANTY; without even the implied warranty of
14 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
15 % General Public License for more details.
16 %
17 % You should have received a copy of the GNU General Public License
18 % along with this program; if not, write to the Free Software
19 % Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
20 % 02110-1301, USA.
21 %
22 % For additional information visit http://murphylab.web.cmu.edu/ or
23 % send email to murphy@cmu.edu
24
25
1 26 if ~isfield(param,'tempparent')
1 27 param.tempparent = [pwd filesep 'temp'];
1 28 end
1 29 if ~exist( param.tempparent,'dir' )
1 30 mkdir( param.tempparent );
1 31 end
32
33
34 %Preprocessed results (segmented cells and nuclei)
1 35 if ~isfield(param,'preprocessingFolder')
1 36 param.preprocessingFolder = [ param.tempparent filesep 'preprocessing' ];
1 37 end
1 38 if ~exist( param.preprocessingFolder,'dir' )
1 39 mkdir( param.preprocessingFolder );
1 40 end
41
42 %Per-cell nuclear features
1 43 if ~isfield(param,'nuctemppath')
1 44 param.nuctemppath = [param.tempparent filesep 'nuclearfeats'];
1 45 end
46
47 %Per-cell cell features
1 48 if ~isfield(param,'celltemppath')
1 49 param.celltemppath = [param.tempparent filesep 'cell_shape_eigen'];
1 50 end
1 51 if ~exist(param.celltemppath,'dir')
1 52 mkdir(param.celltemppath)
0.01 1 53 end
54
55 %Per-cell protein features
56 %default parent directory
1 57 temporaryProtFolder = [ param.tempparent filesep 'protein_objects_gaussian' ];
58
59 %preprocessed objects
1 60 if ~isfield(param,'objtemppath')
1 61 param.objtemppath = [ temporaryProtFolder filesep 'original_objects'];
1 62 end
63
64 %fit objects
1 65 if ~isfield(param,'savefitdir')
1 66 param.savefitdir = [ temporaryProtFolder filesep 'object_gaussians'];
1 67 end
1 68 if ~exist(param.savefitdir,'dir')
1 69 mkdir(param.savefitdir);
1 70 end
71
72 %object stats
1 73 if ~isfield(param,'objstatsdir')
1 74 param.objstatsdir = [temporaryProtFolder filesep 'object_stats' filesep];
1 75 end
76
77 %object sizes
1 78 if ~isfield(param,'objsizedir')
1 79 param.objsizedir = [temporaryProtFolder filesep 'object_sizes' filesep];
1 80 end
81
82 %object positions
1 83 if ~isfield(param,'objposdir')
1 84 param.objposdir = [temporaryProtFolder filesep 'object_positions' filesep];
1 85 end
86
1 87 if ~isfield(param,'compartmentdir')
1 88 param.compartmentdir = [ param.tempparent filesep 'compartment_stats' filesep];
1 89 end
1 90 if ~exist(param.compartmentdir,'dir')
1 91 mkdir(param.compartmentdir);
1 92 end

Other subfunctions in this file are not included in this listing.