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plotNTaxisDataComparison.m
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plotNTaxisDataComparison.m
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clear all, close all
showText = false % true;
% Make sure we have the right coordinates
exportCoordinates()
% These are all coordinates from Retistruct
data = load('allNTcoords.mat');
figNT = figure;
plot([0 1],[0 1],'r-')
figDV = figure;
plot([0 1],[0 1],'r-')
% Reber Email 10 june 2014
%
% 22.2 - 26% NT axis 80% DV axis (where Dorsal = 0% and Ventral = 100%). so this one is a very ventral injection.
% 22.3 - 20% NT axis 48% DV axis
% 22.4 -14% NT axis 23% DV axis
% 22.6 - 13% NT 74% DV
% 22.8 - 33% NT 87% DV
% 22.9 - 8% NT 74% DV
% 32.1 - 88 % NT 23% DV
% 32.2 - 99% NT 33% DV
% First column NT, second column DV
% ReberData = {{'Ret22.2', [22.6 80]}, ...
% {'Ret22.3', [20 48]}, ...
% {'Ret22.4', [14 23]}, ...
% {'Ret22.6', [13 74]}, ...
% {'Ret22.8', [33 87]}, ...
% {'Ret22.9', [8 74]}, ...
% {'Ret32.1', [88 23]}, ...
% {'Ret32.2', [99 33]}, ...
% {'D5.4',[11 67]}, ...
% {'D5.6',[22 55]}, ...
% {'D6.11total',[70 38]}, ...
% {'Ret1C',[32 52]}, ...
% ... % {'Ret2C',[74 52]}, ...
% {'Ret3C',[47 37]} } %, ...
% % {'WT1', [85 78]}, ...
% % {'WT2', [70 59]}, ...
% % {'WT3', [80 58]}};
% Reordered to match colours
ReberData = { {'D5.6',[22 55]}, ...
{'Ret22.2', [22.6 80]}, ...
{'Ret22.3', [20 48]}, ...
{'Ret22.6', [13 74]}, ...
{'Ret22.9', [8 74]}, ...
{'Ret32.2', [99 33]}, ...
{'Ret32.1', [88 23]}, ...
{'Ret22.4', [14 23]}, ...
{'Ret22.8', [33 87]}, ...
{'D5.4',[11 67]}, ...
{'D6.11total',[70 38]}, ...
{'Ret1C',[32 52]}, ...
... % {'Ret2C',[74 52]}, ...
{'Ret3C',[47 37]} } %, ...
sphereNT = NaN*ones(numel(ReberData),1);
sphereDV = NaN*ones(numel(ReberData),1);
retistructNT = NaN*ones(numel(ReberData),1);
retistructDV = NaN*ones(numel(ReberData),1);
for i = 1:numel(ReberData)
ReberName = ReberData{i}{1};
ReberNTproj = ReberData{i}{2}(1) / 100;
ReberDVproj = ReberData{i}{2}(2) / 100;
intactRetinaNT = NaN;
intactRetinaDV = NaN;
% See if intact 3D data exist
fNameMask = sprintf('SAVE/%s*.tif-save.mat',ReberName);
files = dir(fNameMask);
if(numel(files) > 1)
for j = 1:numel(files)
fprintf('Multiple files: %s\n', files(j).name)
end
beep
return
end
% Is there a unique file with data?
if(numel(files) == 1)
fName = sprintf('SAVE/%s', files(1).name);
fprintf('Reading intact retina NT from %s\n', fName)
data3D = load(fName);
intactRetinaNT = data3D.data.topView_injNT;
intactRetinaDV = data3D.data.topView_injDV;
assert(0 <= intactRetinaNT & intactRetinaNT <= 1)
assert(0 <= intactRetinaDV & intactRetinaDV <= 1)
% Save NT and DV for summary CSV file at end
sphereNT(i) = intactRetinaNT;
sphereDV(i) = intactRetinaDV;
end
for j = 1:numel(data.name)
if(strcmpi(ReberName,data.name(j)))
% Save NT and DV for summary CSV file at end
retistructNT(i) = data.NT(j);
retistructDV(i) = data.DV(j);
figure(figNT)
hold on
if(~isnan(ReberNTproj))
pNT(1) = plot(data.NT(j),ReberNTproj,'ko','markersize',10);
if(showText)
text(data.NT(j),ReberNTproj+0.03,ReberName, ...
'fontsize',10,'rotation',90)
end
hold on
fprintf('Plotting: %f, %f\n', data.NT(j), ReberNTproj)
end
if(~isnan(intactRetinaNT))
pNT(2) = plot(data.NT(j),intactRetinaNT,'r.','markersize',20);
if(showText & isnan(ReberNTproj))
text(data.NT(j),intactRetinaNT+0.03,ReberName,...
'fontsize',10,'rotation',90)
end
hold on
fprintf('Plotting: %f, %f\n', data.NT(j), intactRetinaNT)
else
fprintf('Missing %s intact 3D data\n', ReberName)
end
figure(figDV)
hold on
if(~isnan(ReberDVproj))
pDV(1) = plot(data.DV(j),ReberDVproj,'ko','markersize',10);
if(showText)
text(data.DV(j),ReberDVproj+0.03,ReberName, ...
'fontsize',10,'rotation',90)
end
hold on
fprintf('Plotting: %f, %f\n', data.DV(j), ReberDVproj)
end
if(~isnan(intactRetinaDV))
pDV(2) = plot(data.DV(j),intactRetinaDV,'r.','markersize',20);
if(showText & isnan(ReberNTproj))
text(data.DV(j),intactRetinaDV+0.03,ReberName, ...
'fontsize',10, 'rotation',90)
end
hold on
fprintf('Plotting: %f, %f\n', data.DV(j), intactRetinaDV)
end
end
end
end
figure(figNT)
legend(pNT,'Projection method (2D)', ...
'IntactEye (3D)', ...
'location','Northwest');
axis equal
axis([0 1 0 1])
box off
% title('Comparison 3D vs flat')
xlabel('NT axis 3D (retistruct)','fontsize',24)
ylabel('NT axis flat','fontsize',24)
set(gca,'fontsize',20)
saveas(gcf,'FIGS/Reber-compare-methods-NT-axis.pdf','pdf')
figure(figDV)
legend(pDV,'Projection method (2D)', ...
'IntactEye (3D)', ...
'location','Northwest');
axis equal
axis([0 1 0 1])
box off
% title('Comparison 3D vs flat')
xlabel('DV axis 3D (retistruct)','fontsize',24)
ylabel('DV axis flat','fontsize',24)
set(gca,'fontsize',20)
saveas(gcf,'FIGS/Reber-compare-methods-DV-axis.pdf','pdf')
fid = fopen('measure-summary.csv','w');
fprintf(fid,'Name,ReberNT,ReberDV,RetistructNT,RetistructDV,SphereNT,SphereDV\n');
for i = 1:numel(ReberData)
fprintf(fid, '%s,%f,%f,%f,%f,%f,%f\n', ...
ReberData{i}{1}, ...
ReberData{i}{2}(1), ...
ReberData{i}{2}(2), ...
100*retistructNT(i), ...
100*retistructDV(i), ...
100*sphereNT(i), ...
100*sphereDV(i));
end
fclose(fid);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
colours0 = [0 0 0];
colours1 = [166,206,227
31,120,180
178,223,138
51,160,44
251,154,153
227,26,28
253,191,111
255,127,0
202,178,214
106,61,154
... %255,255,153
177,89,40] /255;
colours2 = [141,211,199
...% 255,255,179
...%190,186,218
251,128,114
128,177,211
253,180,98
179,222,105
252,205,229
217,217,217
188,128,189
204,235,197
255,237,111]/255;
colours = [colours0;colours1;colours2]*0.9;
% Lets do two more plots
ReberNT = NaN * ones(numel(ReberData),1);
ReberDV = NaN * ones(numel(ReberData),1);
figure, hold on
plot([0 100],[0 100],'--','color',[1 1 1]*0.3)
for i = 1:numel(ReberData)
ReberNT(i) = ReberData{i}{2}(1);
if(~isnan(ReberData{i}{2}(1)))
plot(ReberData{i}{2}(1)*[1 1],100*[sphereNT(i) retistructNT(i)], ...
'-','color',[1 1 1]*0.8)
if(~isnan(retistructNT(i)))
pR = plot(ReberData{i}{2}(1), 100 * retistructNT(i), ...
'*','markersize',15,'color',colours(i,:));
end
if(~isnan(sphereNT(i)))
p3 = plot(ReberData{i}{2}(1), 100*sphereNT(i), ...
'.','markersize',30,'color',colours(i,:));
end
end
if(i == 1)
pR1 = pR;
p31 = p3;
end
end
legend([pR1 p31], 'Retistruct','IntactEye','location','southeast')
xlabel('Flat NT','fontsize',24)
ylabel('Spherical NT','fontsize',24)
set(gca,'fontsize',20)
box off
axis equal
axis([0 100 0 100])
set(gca,'xtick',0:20:100)
set(gca,'ytick',0:20:100)
saveas(gcf,'FIGS/Reber-compare-methods-NT-axis-alt.pdf','pdf')
pR = []; p3 = [];
figure, hold on
plot([0 100],[0 100],'--','color',[1 1 1]*0.3)
for i = 1:numel(ReberData)
ReberDV(i) = ReberData{i}{2}(2);
if(~isnan(ReberData{i}{2}(2)))
plot(ReberData{i}{2}(2)*[1 1],100*[sphereDV(i) retistructDV(i)], ...
'-','color',[1 1 1]*0.8)
if(~isnan(retistructDV(i)))
pR = plot(ReberData{i}{2}(2), 100 * retistructDV(i), ...
'*','markersize',15,'color',colours(i,:));
end
if(~isnan(sphereDV(i)))
p3 = plot(ReberData{i}{2}(2), 100*sphereDV(i), ...
'.','markersize',30, 'color',colours(i,:));
end
end
if(i == 1)
pR1 = pR;
p31 = p3;
end
end
legend([pR1 p31], 'Retistruct','IntactEye','location','southeast')
xlabel('Flat DV','fontsize',24)
ylabel('Spherical DV','fontsize',24)
set(gca,'fontsize',20)
box off
axis equal
axis([0 100 0 100])
set(gca,'xtick',0:20:100)
set(gca,'ytick',0:20:100)
saveas(gcf,'FIGS/Reber-compare-methods-DV-axis-alt.pdf','pdf')
format compact
% Proj vs IntactEye
CNTPI = corr([ReberNT,sphereNT],'rows','complete');
fprintf('Corr Proj vs IntactEye (NT): %.2f\n', CNTPI(2))
% Proj vs Retistruct
CNTPRS = corr([ReberNT,retistructNT],'rows','complete');
fprintf('Corr Proj vs Retistruct (NT): %.2f\n', CNTPRS(2))
% IntactEye vs Retistruct
CNTIRS = corr([sphereNT,retistructNT],'rows','complete');
fprintf('Corr IntactEye vs Retistruct (NT): %.2f\n', CNTIRS(2))
% Save for DV
CDVPI = corr([ReberDV,sphereDV],'rows','complete');
fprintf('Corr Proj vs IntactEye (DV): %.2f\n', CDVPI(2))
CDVPRS = corr([ReberDV,retistructDV],'rows','complete');
fprintf('Corr Proj vs Retistruct (DV): %.2f\n', CDVPRS(2))
CDVIRS = corr([sphereDV,retistructDV],'rows','complete');
fprintf('Corr IntactEye vs Retistruct (DV): %.2f\n', CDVIRS(2))