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imapLMMdisplay.m
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imapLMMdisplay.m
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function imapLMMdisplay(StatMap,normalized,backgroundfile,cmap,colormaprange,distplot,foldername)
% Usage: imapLMMdisplay(StatMap,normalized,backgroundfile,colourmap,colormaprange,distplot)
% display result after contrast test. Input result from imapLMMcontrast
% input structure format {opt} {Pmap} {Pmask} {F/Tmap} {betamap(optional)}
% {labels of the maps} {MCC related field}
% display map value would be normalized [1] as default
% backgroundfile could be image/matrix/[empty]
% colormap could be predefined
% output distribution of statistic value (optional, default 0)
%
% opt within StatMap:
% opt.type - model/fixed/random/model beta/predictor beta
% opt.alpha - default 0.05
% opt.c - for coefficients and Catepredictors only, cell array
% containing contrast vector/matrix
% opt.h - for coefficients and Catepredictors only, cell array
% containing hypothesis vector/matrix
% opt.onetail - option to do onetail test, perform on two tail threshold
% for convenience (alpha/2)
% opt.name - for coefficients and Catepredictors only, name of each
% contrast (for plotting)
% See also imapLMM, imapLMMcontrast
%
% 2015-02-12 Junpeng Lao, University of Fribourg.
%--------------------------------------------------------------------------
% Copyright (C) iMap Team 2015
%%
scrsz=get(0,'ScreenSize');% get screen size for output display
opt=StatMap.opt;
if nargin<2
normalized=1;
end
if nargin<3
im3D=[];
else %read background map.
if ischar(backgroundfile)&&~isempty(backgroundfile)
imbackground = double(imread(sprintf(backgroundfile)))/255;
elseif isempty(backgroundfile)
im3D=[];
imbackground = [];
else
imbackground = double(backgroundfile)/max(double(backgroundfile(:)));
end
if ~isempty(imbackground)
% transfer background image to gray scale
if size(imbackground,3)>1
im3D = repmat(rgb2gray(imbackground),[1,1,3]);
else
im3D = repmat(imbackground,[1,1,3]);
end
end
end
if nargin<4 || isempty(cmap)
darkness=0.75;
colourmap(:,1)=[linspace(0,1,32) linspace(1,darkness,32)];
colourmap(:,2)=[linspace(0,1,32) linspace(1,0,32)];
colourmap(:,3)=[linspace(darkness,1,32) linspace(1,0,32)];
elseif ischar(cmap)&& ~isempty(cmap)
cmap2=colormap(cmap);
colourmap=cmap2;
end
if nargin<5 || isempty(colormaprange) || isnan(colormaprange)
colormaprange=1;
end
if nargin<6 || isempty(distplot) || isnan(distplot)
distplot=0;
end
if nargin<7
foldername=['imapLMMoutput-' opt.type];
end
label=StatMap.label;
maptemp=StatMap.map;
if ~ismatrix(maptemp)
mask=~isnan(squeeze(sum(maptemp,1)));
else
mask=~isnan(maptemp);
end
cr=colormaprange;
switch opt.type
case 'model'% output model fitting and criterion map
%% create folder
mkdir(foldername)
% Rsquared
figure('NumberTitle','off','Name','R^2 of model','Position',[1 1 scrsz(3) scrsz(4)/2]);
maprangetmp=sort(squeeze(max(abs(maptemp(1:2,mask)))));
mapmax=maprangetmp(round(length(maprangetmp)*cr));
mapmin=min(min(min(maptemp(1:2,mask))));
range1=[-mapmax mapmax];
range2=[mapmin mapmax];
for ip=1:2
subplot(1,2,ip)
toimage=squeeze(maptemp(ip,:,:));
toimage(isnan(toimage)==1)=0;
imshow(toimage,range1,'colormap',colourmap);
h=colorbar;set(h,'ylim',range2)
% axis off
set(gca,'XTick',[],'YTick',[])
title(label{ip})
end
cd(['./' foldername]);print('-depsc2','-r300','R^2 of model');cd('..');
% Model Criterion
figure('NumberTitle','off','Name','Model Criterion','Position',scrsz);
for ip=1:4
toimage=squeeze(maptemp(ip+2,:,:));
% mapabs=max(abs(toimage(:)));
mapmax=max(toimage(:));
mapmin=min(toimage(:));
range2=[mapmin mapmax];
subplot(2,2,ip)
if mapmin>0
toimage(isnan(toimage)==1)=Inf;
end
imshow(toimage,range2,'colormap',colourmap);
h=colorbar;set(h,'ylim',range2)
% axis off
set(gca,'XTick',[],'YTick',[])
title(label{ip+2})
end
cd(['./' foldername]);print('-depsc2','-r300','Model Criterion');cd('..');
if ~isempty(im3D)
im3D2=imresize(im3D,[size(maptemp,2),size(maptemp,3)],'box');
% Rsquared
figure('NumberTitle','off','Name','R^2 of model(with background)','Position',[1 1 scrsz(3) scrsz(4)/2]);
maprangetmp=sort(squeeze(max(abs(maptemp(1:2,mask)))));
mapmax=maprangetmp(round(length(maprangetmp)*cr));
mapmin=min(min(min(maptemp(1:2,mask))));
range1=[-mapmax mapmax];
range2=[mapmin mapmax];
for ip=1:2
subplot(1,2,ip)
toimage=squeeze(maptemp(ip,:,:));
toimage(isnan(toimage)==1)=0;
toimagergb=indtorgb(toimage,range1(1),range1(2),colourmap);
toimage=toimagergb.*0.7+im3D2.*0.3;
imshow(toimage,range1);
% axis off
set(gca,'XTick',[],'YTick',[])
title(label{ip})
end
cd(['./' foldername]);print('-depsc2','-r300','R^2 of model(with background)');cd('..');
% Model Criterion
figure('NumberTitle','off','Name','Model Criterion(with background)','Position',scrsz);
for ip=1:4
toimage=squeeze(maptemp(ip+2,:,:));
% mapabs=max(abs(toimage(:)));
mapmax=max(toimage(:));
mapmin=min(toimage(:));
range2=[mapmin mapmax];
subplot(2,2,ip)
if mapmax<0
toimage(isnan(toimage)==1)=mapmin;
else
toimage(isnan(toimage)==1)=mapmax;
end
toimagergb=indtorgb(toimage,range2(1),range2(2),colourmap);
toimage=toimagergb.*0.7+im3D2.*0.3;
imshow(toimage,range2);
% axis off
set(gca,'XTick',[],'YTick',[])
title(label{ip+2})
end
cd(['./' foldername]);print('-depsc2','-r300','Model Criterion(with background)');cd('..');
end
case 'fixed'% output Fvalue map and mask according to MCC
%% create folder
mkdir(foldername)
% pmptemp=StatMap.Pmap;
msktemp=StatMap.Pmask;
% output Statvalue map, Statvalue map with P<0.05 and Statvalue map
% with mask
maprangetmp=sort(maptemp(~isnan(maptemp(:))));
mapmax=maprangetmp(round(length(maprangetmp)*cr));
% mapmax=max(maptemp(:));
% mapmin=min(maptemp(:));
if ~isempty(im3D)
im3D2=imresize(im3D,[size(maptemp,2),size(maptemp,3)],'box');
end
for ip=1:length(label)
toimage=squeeze(maptemp(ip,:,:));
toimage(isnan(toimage)==1)=0;
% pvaltmp=squeeze(pmptemp(ip,:,:));
masktmp=squeeze(msktemp(ip,:,:));
if sum(masktmp(:))==0
warning('No significant result from the current condition...')
else
figure('NumberTitle','off','Name',label{ip},'Position',[1 1 scrsz(3) scrsz(4)/2]);
maprangetmp1=sort(toimage(:));
mapmax1=maprangetmp1(round(length(maprangetmp1)*cr));
% mapmax1=max(toimage(:));
mapmin1=min(toimage(:));
range2=[mapmin1 mapmax1];
if normalized==1
range1=[-mapmax mapmax];
else
range1=[-mapmax1 mapmax1];
end
subplot(1,2,1);
imshow(toimage,range1,'colormap',colourmap);
h=colorbar;set(h,'ylim',range2)
% axis off
set(gca,'XTick',[],'YTick',[])
title('Statistic value map')
subplot(1,2,2);
toimage2=toimage;
toimage2(bwperim(masktmp))=NaN;
toimagesg=indtorgb(toimage2,range1(1),range1(2),colourmap);
imshow(toimagesg)
set(gca,'XTick',[],'YTick',[])
title('Significant area marked by dark line')
cd(['./' foldername]);print('-depsc2','-r300',genvarname(label{ip}));cd('..');
if ~isempty(im3D)
figure('NumberTitle','off','Name',[label{ip} '(with background)'] ,'Position',[1 1 scrsz(3) scrsz(4)/2]);
subplot(1,2,1);
toimagergb=indtorgb(toimage2,range1(1),range1(2),colourmap);
toimagebg=toimagergb.*0.7+im3D2.*0.3;
imshow(toimagebg,range1);
% axis off
set(gca,'XTick',[],'YTick',[])
title('Statistic value map')
subplot(1,2,2);
hc=imagesc(im3D2,range1);set(hc,'AlphaData',0.25);axis equal;
hold on;
toimage2(~masktmp)=NaN;
contv=linspace(min(toimage2(:)),max(toimage2(:)),6);
if isfinite(contv)
imcontour(toimage2,contv);colorbar;caxis([0 range1(end)])
end
imcontour(1:size(masktmp,2),1:size(masktmp,1),masktmp,1,'k','LineWidth',1);
set(gca,'XTick',[],'YTick',[])
title('Significant area marked by dark line')
cd(['./' foldername]);print('-depsc2','-r300',[genvarname(label{ip}) '(with background)']);cd('..');
end
end
end
case 'random'% output Fvalue map, beta map and mask according to MCC
%% create folder
mkdir(foldername)
% pmptemp=StatMap.Pmap;
msktemp=StatMap.Pmask;
% output Statvalue map, Statvalue map with P<0.05 and Statvalue map
% with mask
maprangetmp=sort(maptemp(~isnan(maptemp(:))));
mapmax=maprangetmp(round(length(maprangetmp)*cr));
mapmin=min(maptemp(:));
for ip=1:length(label)
toimage=squeeze(maptemp(ip,:,:));
toimage(isnan(toimage)==1)=0;
% pvaltmp=squeeze(pmptemp(ip,:,:));
masktmp=squeeze(msktemp(ip,:,:));
if sum(masktmp(:))==0
warning('No significant result from the current condition...')
else
h1=figure('NumberTitle','off','Name',[label{ip} ' tvalue map'],'Position',[1 1 scrsz(3) scrsz(4)/2]);
maprangetmp1=sort(toimage(:));
mapmax1=maprangetmp1(round(length(maprangetmp1)*cr));
% mapmax1=max(toimage(:));
mapmin1=min(toimage(:));
range2=[mapmin1 mapmax1];
if normalized==1
range1=[mapmin mapmax];
else
range1=[-mapmax1 mapmax1];
end
toimage2=toimage;
toimage2(bwperim(masktmp))=0;
% toimagesg=indtorgb(toimage2,range1(1),range1(2),colourmap);
imshow(toimage2,range1,'colormap',colourmap)
h=colorbar;set(h,'ylim',range2)
set(gca,'XTick',[],'YTick',[])
title('Significant area marked by white line')
cd(['./' foldername]);print('-dpng','-r300',genvarname(label{ip}));cd('..');
end
end
case {'predictor beta', 'model beta'} % output F/Tvalue map, beta map, pvalue map, and mask according to MCC
%% create folder
mkdir(foldername)
betatmp=StatMap.beta;
% pmptemp=StatMap.Pmap;
msktemp=StatMap.Pmask;
% output Statvalue map, Statvalue map with P<0.05 and Statvalue map
% with mask
maprangetmp=sort(maptemp(~isnan(maptemp(:))));
mapmax=maprangetmp(round(length(maprangetmp)*cr));
% mapmin=min(maptemp(:));
mapmaxb=max(abs(betatmp(:)));
if ~isempty(im3D)
im3D2=imresize(im3D,[size(maptemp,2),size(maptemp,3)],'box');
end
for ip=1:length(label)
toimage=squeeze(maptemp(ip,:,:));
toimage(isnan(toimage)==1)=0;
toimagebeta=squeeze(betatmp(ip,:,:));
toimagebeta(isnan(toimagebeta)==1)=0;
% pvaltmp=squeeze(pmptemp(ip,:,:));
masktmp=squeeze(msktemp(ip,:,:));
if sum(masktmp(:))==0
warning('No significant result from the current condition...')
else
figure('NumberTitle','off','Name',label{ip},'Position',scrsz);
maprangetmp1=sort(toimage(:));
mapmax1=maprangetmp1(round(length(maprangetmp1)*cr));
mapmin1=min(toimage(:));
range2=[mapmin1 mapmax1];
mapmax1beta=max(toimagebeta(:));
mapmin1beta=min(toimagebeta(:));
range2beta=[mapmin1beta mapmax1beta];
if normalized==1
range1=[-mapmax mapmax];
range1beta=[-mapmaxb mapmaxb];
else
range1=[-mapmax1 mapmax1];
range1beta=[-max(abs(toimagebeta(:))) max(abs(toimagebeta(:)))];
end
subplot(2,2,1);
imshow(toimage,range1,'colormap',colourmap);
h=colorbar;set(h,'ylim',range2)
% axis off
set(gca,'XTick',[],'YTick',[])
title('Statistic value map')
if nansum(toimagebeta(:))~=0
subplot(2,2,3);
imshow(toimagebeta,range1beta,'colormap',colourmap);
h=colorbar;set(h,'ylim',range2beta)
% axis off
set(gca,'XTick',[],'YTick',[])
title('Beta map')
end
subplot(2,2,2);
toimage2=toimage;
toimage2(bwperim(masktmp))=NaN;
toimagesg=indtorgb(toimage2,range1(1),range1(2),colourmap);
imshow(toimagesg)
set(gca,'XTick',[],'YTick',[])
title('Significant area marked by dark line')
if nansum(toimagebeta(:))~=0
subplot(2,2,4);
toimage2beta=toimagebeta;
toimage2beta(bwperim(masktmp))=NaN;
toimagesgbeta=indtorgb(toimage2beta,range1beta(1),range1beta(2),colourmap);
imshow(toimagesgbeta)
set(gca,'XTick',[],'YTick',[])
title('Significant area marked by dark line')
end
cd(['./' foldername]);print('-depsc2','-r300',genvarname(label{ip}));cd('..');
if ~isempty(im3D)
figure('NumberTitle','off','Name',[label{ip} '(with background)'] ,'Position',scrsz);
subplot(2,2,1);
toimagergb=indtorgb(toimage2,range1(1),range1(2),colourmap);
toimagebg=toimagergb.*0.7+im3D2.*0.3;
imshow(toimagebg,range1);
% axis off
set(gca,'XTick',[],'YTick',[])
title('Statistic value map')
if nansum(toimagebeta(:))~=0
subplot(2,2,3);
toimagebgbeta=toimagesgbeta.*0.7+im3D2.*0.3;
imshow(toimagebgbeta,range1beta);
% axis off
set(gca,'XTick',[],'YTick',[])
title('Beta map')
end
subplot(2,2,2)
hc=imagesc(im3D2,range1);set(hc,'AlphaData',0.25);axis equal;
hold on
toimage2(~masktmp)=NaN;
contv=linspace(min(toimage2(:)),max(toimage2(:)),6);
if isfinite(contv)
imcontour(toimage2,contv);colorbar;caxis([0 range1(end)])
end
imcontour(1:size(masktmp,2),1:size(masktmp,1),masktmp,1,'k','LineWidth',1)
set(gca,'XTick',[],'YTick',[])
title('Significant area marked by dark line')
if nansum(toimagebeta(:))~=0
subplot(2,2,4)
hc=imagesc(im3D2,range1);set(hc,'AlphaData',0.25);axis equal;
hold on
toimage2beta(~masktmp)=NaN;
contv=linspace(min(toimage2beta(:)),max(toimage2beta(:)),6);
if isfinite(contv)
imcontour(toimage2beta,contv);colorbar;caxis([0 range1beta(end)])
end
imcontour(1:size(masktmp,2),1:size(masktmp,1),masktmp,1,'k','LineWidth',1);
set(gca,'XTick',[],'YTick',[])
title('Significant area marked by dark line')
end
cd(['./' foldername]);print('-depsc2','-r300',[genvarname(label{ip}) '(with background)']);cd('..');
end
end
end
end
%%
if distplot~=0
subpy=floor(sqrt(length(label)));
subpx=ceil(sqrt(length(label)));
if subpy*subpx<length(label);subpy=subpx;end;
figure('NumberTitle','off','Name','Stat value distribution','Position',scrsz);
for ip=1:length(label)
tmp=squeeze(maptemp(ip,:));
y = tmp(isnan(tmp)==0);
x = linspace(min(y),max(y),200);
subplot(subpy,subpx,ip)
hist(y,x);
% Get histogram patches
ph = get(gca,'children');
% Determine number of histogram patches
N_patches = length(ph);
for i = 1:N_patches
% Get patch vertices
vn = get(ph(i),'Vertices');
% Adjust y location
vn(:,2) = vn(:,2) + 1;
% Reset data
set(ph(i),'Vertices',vn)
end
set(gca,'yscale','log');% Change scale
title(label{ip})
end
cd(['./' foldername]);print('-depsc2','-r300','Map value distribution');cd('..');
if isfield(StatMap,'beta')==1
figure('NumberTitle','off','Name','Beta value distribution','Position',scrsz);
for ip=1:length(label)
tmp=squeeze(maptemp(ip,:));
y = tmp(isnan(tmp)==0);
x = linspace(min(y),max(y),200);
subplot(subpy,subpx,ip)
hist(y,x);
% Get histogram patches
ph = get(gca,'children');
% Determine number of histogram patches
N_patches = length(ph);
for i = 1:N_patches
% Get patch vertices
vn = get(ph(i),'Vertices');
% Adjust y location
vn(:,2) = vn(:,2) + 1;
% Reset data
set(ph(i),'Vertices',vn)
end
set(gca,'yscale','log');% Change scale
title(label{ip})
end
cd(['./' foldername]);print('-depsc2','-r300','Beta value distribution');cd('..');
end
end