/
rit_showmap.m
131 lines (100 loc) · 6.01 KB
/
rit_showmap.m
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
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
function [output] = rit_showmap(background, overlay_image, treshold, varargin)
%HELP
% Copyright 2020-2021 Ivana Labounkova(1,2), Rene Labounek(2), Igor Nestrasil(2,3),
% Jan Odstrcilik(1), Ralf P. Tornow(4), Radim Kolar(1)
% (1) Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
% (2) Division of Clinical Behavioral Neuroscience, Department of Pediatrics, University of Minnesota, Minneapolis, USA
% (3) Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA
% (4) Department of Ophthalmology, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
%
% This file is part of Retina Imaging Toolbox available at: https://github.com/ivanalabounkova/retinaimagingtoolbox
%
% Retina Imaging Toolbox 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 any later version.
%
% Retina Imaging Toolbox 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 Retina Imaging Toolbox. If not, see <https://www.gnu.org/licenses/>.
%
% Papers related to specific RIT functions are listed in the cite_papers.txt file.
%%
defaultAlpha = 0.9;
defaultMask = ones(size(background));
defaultScale = 'lin';
expectedScale = {'lin','log'};
p = inputParser;
addRequired(p,'background', @(x) isnumeric(x) && size(x,1)>1 && size(x,2)>1);
addRequired(p,'overlay_image', @(x) isnumeric(x) && size(x,1)==size(background,1) && size(x,2)==size(background,2));
addRequired(p,'treshold', @(x) isnumeric(x) && isscalar(x));
addOptional(p,'Alpha', defaultAlpha, @(x) isnumeric(x) && isscalar(x) && (x > 0 && x <= 1));
addOptional(p,'Mask', defaultMask, @(x) size(x,1)==size(background,1) && size(x,2)==size(background,2) && ismember([0],ismember((double(x(:)))', [0,1]))==0);
addParameter(p,'Scale',defaultScale,@(x) any(validatestring(x,expectedScale)));
parse(p, background, overlay_image, treshold ,varargin{:});
%%
binarymask = zeros(size(p.Results.background));
binarymask(abs(p.Results.overlay_image)>p.Results.treshold & p.Results.Mask == 1) = 1;
component = p.Results.overlay_image;
intmin = min(component(:));
intmax = max(component(:));
component(abs(component)<p.Results.treshold) = 0;
% figure()
h_bar = colorbar('south', 'AxisLocation', 'out'); caxis([intmin, intmax])
orig_axis = get(h_bar, 'Ticks');
orig_axis = (sort(unique([orig_axis -p.Results.treshold p.Results.treshold])));
cla
switch p.Results.Scale
case 'lin'
norm_component = uint8(((component-intmin)./(intmax-intmin))*255);
%
vls = orig_axis;
vals1 = num2cell(vls);
vals = (arrayfun(@(y) num2str(vals1{y}),1:length(vals1),'UniformOutput',false));
case 'log'
component(component>0) = log(component(component>0));
component(component<0) = -log(-component(component<0));
component(component>log(intmax)) = log(intmax);
component(component<-log(-intmin)) = -log(-intmin);
norm_component = uint8(((component-(-log(-intmin)))./(log(intmax)-(-log(-intmin))))*255);
vls1 = -log(abs(orig_axis(orig_axis<=-1)));
vls2 = log(orig_axis(orig_axis>=1));
val1 = num2cell((orig_axis(orig_axis<=-1)));
val2 = num2cell(orig_axis(orig_axis>=1));
if abs(p.Results.treshold) < 1 && abs(p.Results.treshold)>=0
error('Tresh value is not applicable for log colorbar axis')
return
elseif p.Results.treshold == 1
vls = [vls1(1:end-1), vls2];
vals = [ (arrayfun(@(y) num2str(val1{y}),1:length(val1)-1,'UniformOutput',false)), {[num2str(-abs(p.Results.treshold)) '=' num2str(abs(p.Results.treshold))]}, ((arrayfun(@(y) num2str(val2{y}),2:length(val2),'UniformOutput',false)))];
else
vls = [vls1(1:end-1), vls2];
vals = [ (arrayfun(@(y) num2str(val1{y}),1:length(val1)-1,'UniformOutput',false)), {'-1=1'}, ((arrayfun(@(y) num2str(val2{y}),2:length(val2),'UniformOutput',false)))];
end
end
norm_component = ind2rgb(norm_component, jet(256));
rchannel = norm_component(:,:,1);
gchannel = norm_component(:,:,2);
bchannel = norm_component(:,:,3);
background_norm = (p.Results.background - min(p.Results.background(:)))./(max(p.Results.background(:))-min(p.Results.background(:)));
vizual_r = background_norm;
vizual_g = background_norm;
vizual_b = background_norm;
vizual_grey = cat(3, vizual_r, vizual_g, vizual_b);
vizual_r(logical(binarymask)) = rchannel(logical(binarymask));
vizual_g(logical(binarymask)) = gchannel(logical(binarymask));
vizual_b(logical(binarymask)) = bchannel(logical(binarymask));
vizual = cat(3, vizual_r, vizual_g, vizual_b);
component_data=component;
component_data = uint8(((component-intmin)./(intmax-intmin))*255);
first_viz = imshow(vizual_grey, []);
hold on
viz_over = imshow(vizual, []);
set(viz_over, 'Alphadata', p.Results.Alpha)
component_transp = imshow(component_data); set(component_transp, 'Alphadata', 0.01); colormap jet;
h_bar = colorbar('south', 'AxisLocation', 'out','Ticks',vls,'TickLabels',vals); abc = get(h_bar, 'Position'); set(h_bar, 'Position', [abc(1)-0.0 abc(2)-0.08 abc(3) abc(4)*5/6]);
caxis([vls(1,1) vls(1,end)])
end