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percellparam (202 calls, 57685.230 sec)
Generated 05-Nov-2014 07:52:31 using cpu time.
function in file /usr0/home/jenkins/workspace/cellorganizer-demo3D11-glnx64/utilities/3D/percellparam.m
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Parents (calling functions)
Function Name | Function Type | Calls |
img2model | function | 202 |
Lines where the most time was spent
Line Number | Code | Calls | Total Time | % Time | Time Plot |
53 | seg_cell_and_nucleus( ... | 202 | 41357.375 s | 71.7% |  |
76 | cellfit_percell( ... | 202 | 16262.424 s | 28.2% |  |
71 | spfeattmp = tp_nucimgfeat(curr... | 202 | 65.180 s | 0.1% |  |
52 | if ~exist( currentSegfile, 'fi... | 202 | 0.160 s | 0.0% |  |
49 | currentSegfile = [param.prepro... | 202 | 0.090 s | 0.0% |  |
All other lines | | | 0 s | 0% |  |
Totals | | | 57685.230 s | 100% | |
Children (called functions)
Function Name | Function Type | Calls | Total Time | % Time | Time Plot |
seg_cell_and_nucleus | function | 202 | 41357.345 s | 71.7% |  |
cellfit_percell | function | 202 | 16262.414 s | 28.2% |  |
tp_nucimgfeat | function | 202 | 65.150 s | 0.1% |  |
filesep | function | 202 | 0.050 s | 0.0% |  |
num2str | function | 202 | 0.040 s | 0.0% |  |
Self time (built-ins, overhead, etc.) | | | 0.230 s | 0.0% |  |
Totals | | | 57685.230 s | 100% | |
Code Analyzer results
Line number | Message |
71 | The value assigned to variable 'spfeattmp' might be unused. |
Coverage results
[ Show coverage for parent directory ]
Total lines in function | 101 |
Non-code lines (comments, blank lines) | 85 |
Code lines (lines that can run) | 16 |
Code lines that did run | 8 |
Code lines that did not run | 8 |
Coverage (did run/can run) | 50.00 % |
Function listing
time calls line
1 function percellparam( imdna_path,imcell_path,...
2 improt_path,immask_path,cellnum, param )
3 %Parameterizes an image of a cell for use in the CellOrganizer suite.
4 %
5 %Inputs
6 %imdna_path - cell array of image files for dna parameter extraction
7 %imcell_path - cell array of image files for cell parameter extraction
8 % (optional if param.train.flag = 'nuclear')
9 %improt_path - cell array of image files for protein parameter extraction
10 % (optional if param.train.flag = 'nuclear' or 'framework')
11 %immask_path - cell array of image files for masking a single cell
12 % from a given image (these are always optional and can
13 % be passed in as an array of [])
14 %param a structure holding possible parameter options. This
15 % struct should also contain all temporary results
16 % folders.(see set_temp_result_folders.m)
17
18 % Author: Devin Sullivan 6/13/13
19 %
20 % Copyright (C) 2007-2013 Murphy Lab
21 % Carnegie Mellon University
22 %
23 %
24 % This program is free software; you can redistribute it and/or modify
25 % it under the terms of the GNU General Public License as published
26 % by the Free Software Foundation; either version 2 of the License,
27 % or (at your option) any later version.
28 %
29 % This program is distributed in the hope that it will be useful, but
30 % WITHOUT ANY WARRANTY; without even the implied warranty of
31 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
32 % General Public License for more details.
33 %
34 % You should have received a copy of the GNU General Public License
35 % along with this program; if not, write to the Free Software
36 % Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
37 % 02110-1301, USA.
38 %
39 % For additional information visit http://murphylab.web.cmu.edu/ or
40 % send email to murphy@cmu.edu
41
42 % Gregory Johnson 6/17/13
43 % Modified for single image
44 % Shortened some variable names
45 % Formatted for readability
46
47
48 %First perform the segmentation if it doesn't exist
0.09 202 49 currentSegfile = [param.preprocessingFolder filesep 'cell'...
50 num2str(cellnum) '.mat'];
51
0.16 202 52 if ~exist( currentSegfile, 'file' )
41357.38 202 53 seg_cell_and_nucleus( ...
54 imdna_path, ...
55 imcell_path, ...
56 improt_path, ...
57 immask_path, ...
58 param.model.downsampling, ...
59 param.display, ...
60 param, ...
61 cellnum );
62 else
63 if param.verbose
64 disp( [ 'Temporary file ' currentSegfile ' found. Skipping ' ...
65 'image preprocessing.' ] );
66 end
67 end
68
69
70 %Compute Nuclear image feats for each file.
65.18 202 71 spfeattmp = tp_nucimgfeat(currentSegfile,...
72 'cylsurf', param,cellnum );
73
74 %Now get the Cell level parameters
202 75 if strcmpi(param.train.flag,'all')||strcmpi(param.train.flag,'framework')
16262.42 202 76 cellfit_percell( ...
77 imdna_path, ...
78 imcell_path, ...
79 improt_path, ...
80 immask_path, ...
81 param, ...
82 cellnum );
201 83 end
84
85 %Now compute the protein models.
201 86 if strcmpi(param.train.flag,'all')
87 protfit_percell( ...
88 imdna_path, ...
89 imcell_path, ...
90 improt_path, ...
91 immask_path, ...
92 param, ...
93 cellnum );
94
95 %Lastly use any preprocessed results to create compartment
96 %models
97 compartment_percell( ...
98 improt_path, ...
99 param, ...
100 cellnum)
101 end
Other subfunctions in this file are not included in this listing.