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extract_radius_ratio (201 calls, 6.649 sec)
Generated 05-Nov-2014 07:53:25 using cpu time.
function in file /usr0/home/jenkins/workspace/cellorganizer-demo3D11-glnx64/utilities/3D/vesicles/3D/extract_radius_ratio.m
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Parents (calling functions)

Function NameFunction TypeCalls
cellfit_percellfunction201
Lines where the most time was spent

Line NumberCodeCallsTotal Time% TimeTime Plot
87
save(cellcodepath,'rad_ratio',...
2014.456 s67.0%
50
load(fname)
2011.612 s24.2%
63
curr_nuc = interp1(h,curr_nuc,...
1080.120 s1.8%
48
if exist(fname,'file')
2010.090 s1.4%
70
nucelldist = [nucelldist;curr_...
30150.060 s0.9%
All other lines  0.310 s4.7%
Totals  6.649 s100% 
Children (called functions)

Function NameFunction TypeCallsTotal Time% TimeTime Plot
interp1function2160.150 s2.3%
Self time (built-ins, overhead, etc.)  6.499 s97.7%
Totals  6.649 s100% 
Code Analyzer results
Line numberMessage
37The value assigned to variable 'n' might be unused.
42The value assigned to variable 'distratio' might be unused.
47Use of brackets [] is unnecessary. Use parentheses to group, if needed.
51The value assigned to variable 'baseplane' might be unused.
54The value assigned to variable 'stack' might be unused.
55Variable 'cellcodes' is used, but might be unset.
62The variable 'curr_nuc' appears to change size on every loop iteration. Consider preallocating for speed.
65The variable 'curr_cell' appears to change size on every loop iteration. Consider preallocating for speed.
69The variable 'nucdist' appears to change size on every loop iteration. Consider preallocating for speed.
70The variable 'nucelldist' appears to change size on every loop iteration. Consider preallocating for speed.
89Best practice is for CATCH to be followed by an identifier that gets the error information.
Coverage results
[ Show coverage for parent directory ]
Total lines in function90
Non-code lines (comments, blank lines)52
Code lines (lines that can run)38
Code lines that did run35
Code lines that did not run3
Coverage (did run/can run)92.11 %
Function listing
   time   calls  line
1 function [rad_ratio,cellnucratios,nucbottomslices] = extract_radius_ratio(cellcodepath)
2 % From the cellcodes, extract the radius ratio of nuclear radius over cell
3 % radius under cylindrical systerm
4
5 % Author: Tao Peng
6 % Edited: Ivan E. Cao-Berg
7
8 % June 10 2013 D. Sullivan This method now precomputes radius ratio
9 % statistics per-cell
10 % extract_radius_ratiomodel compiles the model
11 %
12 % Copyright (C) 2011 Murphy Lab
13 % Lane Center for Computational Biology
14 % School of Computer Science
15 % Carnegie Mellon University
16 %
17 % This program is free software; you can redistribute it and/or modify
18 % it under the terms of the GNU General Public License as published
19 % by the Free Software Foundation; either version 2 of the License,
20 % or (at your option) any later version.
21 %
22 % This program is distributed in the hope that it will be useful, but
23 % WITHOUT ANY WARRANTY; without even the implied warranty of
24 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
25 % General Public License for more details.
26 %
27 % You should have received a copy of the GNU General Public License
28 % along with this program; if not, write to the Free Software
29 % Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
30 % 02110-1301, USA.
31 %
32 % For additional information visit http://murphylab.web.cmu.edu or
33 % send email to murphy@cmu.edu
34
35 % Constants
36 %protype = {'DNA','LAM','Nuc','Gia','Gpp','Mit','TfR'};
201 37 n = 360;
0.02 201 38 H = -pi:(2*pi/360):pi;
201 39 k = 0;
40
41 % Calculate radius ratios and combining them
201 42 distratio = []; cellnucratios = []; nucbottomslices = [];
43 % celllist = ml_dir([cellcodepath filesep 'cellcodes_*']);
44
45 % for i = 1:length(celllist)
46 % fname = [cellcodepath filesep celllist{i}];
201 47 fname = [cellcodepath];
0.09 201 48 if exist(fname,'file')
0.01 201 49 k = k + 1;
1.61 201 50 load(fname)
201 51 baseplane(k) = equatorZ;
201 52 nucdist = [];
201 53 nucelldist = [];
0.01 201 54 stack = [];
201 55 for s = 1:length(cellcodes)
56 % disp(['s:' num2str(s)]);
0.04 3015 57 if ~isempty(cellcodes{s})
0.05 3015 58 curr_nuc = cellcodes{s}.nucdist;
0.02 3015 59 curr_cell = cellcodes{s}.nucelldist;
0.02 3015 60 if length(curr_nuc) ~= 360
108 61 h = -pi:(2*pi/length(curr_nuc)):pi;
108 62 curr_nuc(end+1) = curr_nuc(1);
0.12 108 63 curr_nuc = interp1(h,curr_nuc,H);
108 64 curr_nuc(end) = [];
108 65 curr_cell(end+1) = curr_cell(1);
0.03 108 66 curr_cell = interp1(h,curr_cell,H);
108 67 curr_cell(end) = [];
108 68 end
0.06 3015 69 nucdist = [nucdist;curr_nuc];
0.06 3015 70 nucelldist = [nucelldist;curr_cell];
3015 71 end
0.01 3015 72 end
0.02 201 73 r = nucdist ./ nucelldist;
201 74 distratio = r(:);
201 75 rad_ratio = distratio';
76 % cellnucratios = [cellnucratios;cellnucheightratio];
77 % nucbottomslices = [nucbottomslices;nucbottomslice];
78 else
79 error([cellcodepath ' does not exist, cannot compute radius ratio.']);
80 end
81 % end
82
83
84
201 85 try
86 % save('./temp/cell_shape_eigen/radius_ratio.mat','rad_ratio','cellnucratios','nucbottomslices')
4.46 201 87 save(cellcodepath,'rad_ratio','nucdist','nucelldist','cellnucheightratio','nucbottomslice','cellcodes','equatorZ')
88
89 catch
201 90 end