ObjectFinder/calcPathLengthStats.m at master · UCSFVisionResearch/ObjectFinder · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
%% ObjectFinder - Recognize 3D structures in image stacks
%  Copyright (C) 2016,2017,2018 Luca Della Santina
%
%  This file is part of ObjectFinder
%
%  ObjectFinder 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 3 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, see <https://www.gnu.org/licenses/>.
%
function PathLengthStats = calcPathLengthStats(Dots, Skel, showPlot)

Dots = getFilteredObjects(Dots, Dots.Filter); % work only on validated objects

DotPathLengthList   = Skel.FilStats.SkelPathLength2Soma(Dots.Skel.ClosestSkelIDs);
EdgePathLengthList  = Skel.FilStats.EdgePathLength2Soma;
EdgeLengthList      = Skel.SegStats.Lengths;

EdgePathLengthMax   = ceil(max(EdgePathLengthList));

DistBin             = 10; %Bin distance is 10 micron by default
DistFromSoma        = 5:1:EdgePathLengthMax;
NumDots             = zeros(1, length(DistFromSoma));
EdgeLengths         = zeros(1, length(DistFromSoma));
for i = 1 : length(DistFromSoma)
    NumDots(i)      = length(find((DotPathLengthList>DistFromSoma(i)-DistBin/2) & (DotPathLengthList<=DistFromSoma(i)+DistBin/2)));
    EdgeLengths(i)  = sum(EdgeLengthList((EdgePathLengthList>DistFromSoma(i)-DistBin/2) & (EdgePathLengthList<=DistFromSoma(i)+DistBin/2)));
end

PathLengthStats.PathLengthBin       = DistBin;
PathLengthStats.PathLength2CB       = DistFromSoma;
PathLengthStats.PvsPathLength       = NumDots;
PathLengthStats.DvsPathLength       = EdgeLengths;
PathLengthStats.PoverDvsPathLength  = NumDots./EdgeLengths;

if showPlot
    width   = 20;
    height  = 20;
    set(0,'units','centimeters');
    scrsz   = get(0,'screensize');
    position= [scrsz(3)/2-width/2 scrsz(4)/2-height/2 width height];
    h       = figure;
    set(h,'units','centimeters');
    set(h,'position',position);
    set(h,'paperpositionmode','auto');
    set(0,'units','pixel');
    set(h,'units','pixel');
    set(gcf, 'Color', [0 0 0]);

    subplot(3,1,1, 'Color', [0 0 0]), hold on;
    plot(DistFromSoma, NumDots, 'w', 'LineWidth', 2);
    axis([0 EdgePathLengthMax 0 250]);
    set(gca, 'XColor', [1 1 1]); set(gca, 'YColor', [1 1 1]);
    title('bin=10um');
    xlabel('Path length from cell body (µm)');
    ylabel('Total number of dots in the bin');

    subplot(3,1,2, 'Color', [0 0 0]), hold on;
    plot(DistFromSoma, EdgeLengths, 'w', 'LineWidth', 2);
    axis([0 EdgePathLengthMax 0 400]);
    set(gca, 'XColor', [1 1 1]); set(gca, 'YColor', [1 1 1]);
    title('bin=10um');
    xlabel('Path length from cell body (µm)');
    ylabel('Total lengths of dendrites in the bin');

    subplot(3,1,3, 'Color', [0 0 0]), hold on;
    plot(DistFromSoma, PoverD, 'w', 'LineWidth', 2);
    axis([0 EdgePathLengthMax 0 max(1, max(PoverD))]);
    set(gca, 'XColor', [1 1 1]); set(gca, 'YColor', [1 1 1]);
    title('bin=10um');
    xlabel('Path length from cell body (µm)');
    ylabel('#puncta/µm dendrite');

    set(gcf,'inverthardcopy','off'); %this will prevent color change back to default upon saving or printing
    %saveas(gcf, [pwd filesep 'images' filesep 'DotDend_vs_PathLengthStats'], 'tif');
end
end