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GEKO_opensourcev8.m
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GEKO_opensourcev8.m
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function GEKO_opensourcev7
% GEKO is an automated GUI to evaluate knee OA in frontally sectioned
% rodent histological images. It calculates 8 of the 10 OARSI recommended
% grades from the OARSI histopathology initiative (Gerwin 2010).
%% FUNCTION NOTES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% lines can be set to 'hide' or 'show' to have lines appear as you draw them
% or to suppress the lines
% wfile is the file name for summary file, should include extension. IE 'GEKO_Summary.xls'
% getptsNoDoubleClick was provided at
% https://cbi.nyu.edu/svn/mrTools/trunk/mrUtilities/MatlabUtilities/
% by the NYU CBI (info@cbi.nyu.edu)
%% EDIT LOG %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% BYMJ 6/15/17: Added back button and disabled getpts double-click to end
% selection. Fixed so that images may be selected from any folder (does not
% have to be in same location as GEKO function). Fixed file name finding
% for general case. Added try loop and error catching. Cleaned up comments.
% Added comments. Adjusted calculations to account for getpts change.
% BYMJ 6/16/17: Added dialogue box questions to set initial parameters and
% remove all print to command line information to prep for .exe packaging.
% Added zoom functionality.
%%
% Turns off warnings for the session - BYMJ
warning('off','all')
warning
% Creates question dialogue box to set lines mode. Hide setting is selected
% as default. - BYMJ
choice = questdlg('Show or hide output lines during grading?', ...
'Set Lines', ...
'show','hide','hide');
% Handle response
switch choice
case 'show'
lines = 'show';
case 'hide'
lines = 'hide';
end
% Requests user set a summary file name. -BYMJ
prompt = {'Enter desired summary file name'};
dlg_title = 'Summary title';
num_lines = 1;
defaultans = {'GEKO_Summary.xls'};
answer = inputdlg(prompt,dlg_title,num_lines,defaultans);
wfile = answer{1};
% Give users instruction to select image files. -BYMJ
waitfor(msgbox({'Please select images to grade.' 'Use shift + left mouse to select more than one file.',...
'Files may only be selected from one directory at a time.'},'Select Image Help'));
% Select image files to work with
[fname1,pname1]=uigetfile({'*.*';'*.jpg';'*.png';'*.tiff'},'Select Image(s)','MultiSelect', 'on');
% This is needed for the multiselect. Always put the file in this format.
% -BYMJ
fname1 = cellstr(fname1);
% Import Reference Images
OARSI1 = imread('OARSI1.png');
OARSI2 = imread('OARSI2.png');
OARSI3 = imread('OARSI3.png');
OARSI4 = imread('OARSI4.png');
OARSI5 = imread('OARSI5.png');
OARSI6 = imread('OARSI6.png');
OARSI7 = imread('OARSI7.png');
OARSI8 = imread('OARSI8.png');
OARSI9 = imread('OARSI9.png');
Lablogo = imread('Lablogo.jpg');
% This for loop steps through each selected file. -BYMJ
for p = 1:length(fname1) % This for loop and everything before this line should be part of the GEKO shell code. -BYMJ
try % If a file crashes, continue on to the next file in "fname1". -BYMJ
% Store current filename. -BYMJ
filename = fullfile ( pname1, fname1{p} );
% Break up filename into path, name, and extension.
[~,name,~] = fileparts(filename);
% Read in the current file and set an identifier for the trial. -BYMJ
I = imread(filename);
ID = name;
[r, c, ~] = size(I);
%% Create the marking points
% Variable to indicate whether a regrade is needed. -BYMJ
redo = 'y';
while redo == 'y'
redo = 'n'; % Assume the image will not need to be regraded until the user inputs otherwise. -BYMJ
% Create the Main GUI figure. -BYMJ
figure('units','normalized','outerposition',[0 0 1 1])
hold on
set(gcf,'Color','w');
% Plot the reference image. -BYMJ
subplot(3,4,1), image(OARSI1); axis off
title('Reference Image')
axis image
% Display the OrthoBME logo. -BYMJ
subplot(3,4,9), image(Lablogo); axis off
axis image
subplot(3,4,[2:4,6:8,10:12]), image(I)
ax = gca;
title(ID,'interpreter','none')
axis image
linethick = 2;
% Define tibial plateau
clear px1 py1
t1 = subplot(3,4,5, 'replace');
fixfont = text(0,0,sprintf('Please click the \ntwo endpoints defining \nthe tibial plateau. \n \nPress ENTER to end.'), 'Parent', t1); axis off
fixfont.FontSize = 16;
[px1, py1] = getptsNoDoubleClick(ax);
hold on
if exist('px1','var')
subplot(3,4,[2:4,6:8,10:12]), plot(px1,py1,'ko');
end
% Store x and y coordinates in a structure to save later.
rawpoints.tibplateauX = px1;
rawpoints.tibplateauY = py1;
linecomp = strcmp(lines,'show');
if linecomp == 1
subplot(3,4,[2:4,6:8,10:12]), plat = plot(px1,py1,'k');
set(plat,'LineWidth',linethick);
end
% Define joint capsule thickness
clear sx1 sy1
subplot(3,4,1), image(OARSI2), axis off
title('Reference Image')
axis image
t1 = subplot(3,4,5,'replace');
fixfont = text(0,0,sprintf('Please click the \ntwo endpoints defining \nthe joint capsule. \n \nPress ENTER to end.'), 'Parent', t1); axis off
fixfont.FontSize = 16;
[sx1, sy1] = getptsNoDoubleClick(ax);
hold on
if exist('sx1','var')
subplot(3,4,[2:4,6:8,10:12]), plot(sx1,sy1,'go');
end
rawpoints.jointcapsuleX = sx1;
rawpoints.jointcapsuleY = sy1;
linecomp = strcmp(lines,'show');
if linecomp == 1
subplot(3,4,[2:4,6:8,10:12]), plat = plot(sx1,sy1,'g');
set(plat,'LineWidth',linethick);
end
% Define growth plate medial and lateral thickness
clear mgpx1 mgpy1 lgpx1 lgpy1
subplot(3,4,1), image(OARSI3), axis off
title('Reference Image')
axis image
t1 = subplot(3,4,5,'replace');
fixfont = text(0,0,sprintf('Please click the \ntwo endpoints defining the \nthickness of the medial half \nof the medial compartment \ngrowth plate. \n \nPress ENTER to end.'), 'Parent', t1); axis off
fixfont.FontSize = 16;
[mgpx1, mgpy1] = getptsNoDoubleClick(ax);
hold on
if exist('mgpx1','var')
subplot(3,4,[2:4,6:8,10:12]), plot(mgpx1,mgpy1,'mo');
end
rawpoints.medgrowthplateX = mgpx1;
rawpoints.medgrowthplateY = mgpy1;
linecomp = strcmp(lines,'show');
if linecomp == 1
subplot(3,4,[2:4,6:8,10:12]), plat = plot(mgpx1,mgpy1,'m');
set(plat,'LineWidth',linethick);
end
subplot(3,4,1), image(OARSI4), axis off
title('Reference Image')
axis image
t1 = subplot(3,4,5,'replace');
fixfont = text(0,0,sprintf('Please click the two \nendpoints defining the \nthickness of the lateral half \nof the medial compartment \ngrowth plate. \n \nPress ENTER to end.'), 'Parent', t1); axis off
fixfont.FontSize = 16;
[lgpx1, lgpy1] = getptsNoDoubleClick(ax);
hold on
if exist('lgpx1','var')
subplot(3,4,[2:4,6:8,10:12]), plot(lgpx1,lgpy1,'mo');
end
rawpoints.latgrowthplateX = lgpx1;
rawpoints.latgrowthplateY = lgpy1;
linecomp = strcmp(lines,'show');
if linecomp == 1
subplot(3,4,[2:4,6:8,10:12]), plat = plot(lgpx1,lgpy1,'m:');
set(plat,'LineWidth',linethick);
end
%Trace osteochondral interface
clear ocx1 ocy1
subplot(3,4,1), image(OARSI5), axis off
title('Reference Image')
axis image
% % Allows you to zoom in and out on the image. - BYMJ
% t1 = subplot(3,4,5, 'replace');
% fixfont = text(0,0,sprintf('Click and \ndrag an ROI \nto zoom in on \nif desired. \nEnter to continue.'),...
% 'Parent', t1); axis off
% fixfont.FontSize = 16;
%
% zoom on;
% pause() % you can zoom with your mouse and when your image is okay, you press any key. -BYMJ
% zoom off; % to escape the zoom mode -BYMJ
t1 = subplot(3,4,5,'replace');
fixfont = text(0,0,sprintf('Please trace the \nosteochondral interface. \n \nPress ENTER to end.'), 'Parent', t1); axis off
fixfont.FontSize = 16;
clear ocy ocx1 ocy1
[ocx1, ocy1] = getptsNoDoubleClick(ax);
hold on
if exist('ocx1','var')
ocx = zeros(size(ocx1,1),1);
ocy = zeros(size(ocy1,1),1);
for i = 1:size(ocx1,1)
ocx(i) = ocx1(i);
ocy(i) = ocy1(i);
end
subplot(3,4,[2:4,6:8,10:12]), plot(ocx,ocy,'yo');
end
rawpoints.osteointerfaceX = ocx1;
rawpoints.osteointerfaceY = ocy1;
linecomp = strcmp(lines,'show');
if linecomp == 1
subplot(3,4,[2:4,6:8,10:12]), oc = plot(ocx,ocy,'y');
set(oc,'LineWidth',linethick);
end
zoom out;
% Define total cartilage degeneration width
clear tcdwx1 tcdwy1
subplot(3,4,1), image(OARSI6), axis off
title('Reference Image')
axis image
% % Allows you to zoom in and out on the image. - BYMJ
% t1 = subplot(3,4,5, 'replace');
% fixfont = text(0,0,sprintf('Click and \ndrag an ROI \nto zoom in on \nif desired. \nEnter to continue.'),...
% 'Parent', t1); axis off
% fixfont.FontSize = 16;
%
% zoom on; % This will allow zoom once to degenerated ROI. Zoom out will occur after all lesion features are identified. -BYMJ
% pause()
% zoom off;
t1 = subplot(3,4,5,'replace');
fixfont = text(0,0,sprintf('If present, please click \nthe two endpoints defining \nthe total cartilage degeneration \nwidth. \n \nPress ENTER to end. \n \nIf not present, \npress ENTER to skip.'), 'Parent', t1); axis off
fixfont.FontSize = 16;
[tcdwx1, tcdwy1] = getptsNoDoubleClick(ax);
hold on
if exist('tcdwx1','var')
subplot(3,4,[2:4,6:8,10:12]), plot(tcdwx1,tcdwy1,'co');
end
rawpoints.totalcartdegenX = tcdwx1;
rawpoints.totalcartdegenY = tcdwy1;
linecomp = strcmp(lines,'show');
if linecomp == 1
if exist('tcdwx1','var')
if size(tcdwx1)>0
subplot(3,4,[2:4,6:8,10:12]), plat = plot(tcdwx1,tcdwy1,'c');
set(plat,'LineWidth',linethick);
end
end
end
% Define significant cartilage degeneration width
clear scdwx1 scdwy1
subplot(3,4,1), image(OARSI7), axis off
title('Reference Image')
axis image
t1 = subplot(3,4,5,'replace');
fixfont = text(0,0,sprintf('If present, please click \nthe two endpoints defining \nthe significant cartilage \ndegeneration width. \n \nPress ENTER to end. \n \nIf not present, press \nENTER to skip.'), 'Parent', t1); axis off
fixfont.FontSize = 16;
[scdwx1, scdwy1] = getptsNoDoubleClick(ax);
hold on
if exist('scdwx1','var')
subplot(3,4,[2:4,6:8,10:12]), plot(scdwx1,scdwy1,'bo');
end
rawpoints.sigcartdegenX = scdwx1;
rawpoints.sigcartdegenY = scdwy1;
linecomp = strcmp(lines,'show');
if linecomp == 1
if exist('scdwx1','var')
if size(scdwx1)>0
subplot(3,4,[2:4,6:8,10:12]), plat = plot(scdwx1,scdwy1,'b:');
set(plat,'LineWidth',linethick);
end
end
end
% Define cartilage lesion
subplot(3,4,1), image(OARSI8), axis off
title('Reference Image')
axis image
clear cx cy cx1 cy1
t1 = subplot(3,4,5,'replace');
fixfont = text(0,0,sprintf('If present, trace \nthe cartilage lesion. \n \nPress ENTER to end. \n \nIf not present, press \nENTER to skip.'), 'Parent', t1); axis off
fixfont.FontSize = 16;
[cx1, cy1] = getptsNoDoubleClick(ax);
hold on
if size(cx1,1)>0
cx = zeros(size(cx1,1),1);
cy = zeros(size(cy1,1),1);
for i = 1:size(cx1,1)
cx(i) = cx1(i);
cy(i) = cy1(i);
end
subplot(3,4,[2:4,6:8,10:12]), plot(cx,cy,'ro');
end
rawpoints.lesionX = cx1;
rawpoints.lesionY = cy1;
linecomp = strcmp(lines,'show');
if linecomp == 1
if exist('cx','var')
subplot(3,4,[2:4,6:8,10:12]), fill(cx,cy,'r');
else
subplot(3,4,[2:4,6:8,10:12]);
end
else
subplot(3,4,[2:4,6:8,10:12]);
end
zoom out;
%Define osteophyte thickness
clear ostx1 osty1
subplot(3,4,1), image(OARSI9), axis off
title('Reference Image')
axis image
t1 = subplot(3,4,5,'replace');
fixfont = text(0,0,sprintf('If present, please click \nthe two endpoints defining \nthe thickest diameter \nof the osteophyte. \n \nPress ENTER to end. \n \nIf not present, press \nENTER to skip.'), 'Parent', t1); axis off
fixfont.FontSize = 16;
[ostx1, osty1] = getptsNoDoubleClick(ax);
hold on
if exist('ostx1','var')
if size(ostx1)>0
subplot(3,4,[2:4,6:8,10:12]), plot(ostx1,osty1,'yo');
end
end
rawpoints.osteophyteX = ostx1;
rawpoints.osteophyteY = osty1;
linecomp = strcmp(lines,'show');
if linecomp == 1
if exist('ostx1','var')
subplot(3,4,[2:4,6:8,10:12]), plat = plot(ostx1,osty1,'y:');
set(plat,'LineWidth',linethick);
end
end
% Plot all lines if the user wanted hidden lines during grading.
linecomp = strcmp(lines,'show');
if linecomp == 0
hold on
subplot(3,4,[2:4,6:8,10:12]), plat = plot(px1,py1,'k');
set(plat,'LineWidth',linethick);
subplot(3,4,[2:4,6:8,10:12]), plat = plot(sx1,sy1,'g');
set(plat,'LineWidth',linethick);
subplot(3,4,[2:4,6:8,10:12]), plat = plot(mgpx1,mgpy1,'m');
set(plat,'LineWidth',linethick);
subplot(3,4,[2:4,6:8,10:12]), plat = plot(lgpx1,lgpy1,'m:');
set(plat,'LineWidth',linethick);
subplot(3,4,[2:4,6:8,10:12]), oc = plot(ocx,ocy,'y');
set(oc,'LineWidth',linethick);
if exist('tcdwx1','var')
if size(tcdwx1)>0
subplot(3,4,[2:4,6:8,10:12]), plat = plot(tcdwx1,tcdwy1,'c');
set(plat,'LineWidth',linethick);
end
end
if exist('scdwx1','var')
if size(scdwx1)>0
subplot(3,4,[2:4,6:8,10:12]), plat = plot(scdwx1,scdwy1,'b:');
set(plat,'LineWidth',linethick);
end
end
if exist('cx','var')
if size(cx)>0
subplot(3,4,[2:4,6:8,10:12]), fill(cx,cy,'r');
end
end
if exist('ostx1','var')
if size(ostx1)>0
subplot(3,4,[2:4,6:8,10:12]), plat = plot(ostx1,osty1,'y:');
set(plat,'LineWidth',linethick);
end
end
end
% Creates question dialogue box to regrade image. No is selected
% as default. - BYMJ
choice = questdlg('Would you like to regrade the image?', ...
'Regrade', ...
'yes','no','no');
% Handle response
switch choice
case 'yes'
redo = 'y';
clear rawpoints
case 'no'
redo = 'n';
end
end
%% Begin processing collected data
% Create a waitbar so user knows the code is running. -BYMJ
wait = waitbar(0,'Processing data. Please wait.','WindowStyle','modal');
% Save graded image.
saveas(gcf,fullfile(pname1, [ID '.png']), 'png');
close
waitbar(1/10);
% Save rawpoints structure and clear the variable. -BYMJ
save(ID,'rawpoints');
clear rawpoints
waitbar(2/10);
% This would be the place to move calculations into a separate function
% that loads the necessary variables and processes and saves the data.
% -BYMJ
%% 1. Cartilage Matrix Loss Width (0%, 50%, and 100% lesion depth)
plateau = sqrt((px1(1)-px1(2))^2+(py1(1)-py1(2))^2);
theta = atand((py1(1)-py1(2))/(px1(1)-px1(2)));
if exist('cx','var')
%Determining whether tibial line (black) is above or below lesion)
m = (py1(2)-py1(1))/(px1(2)-px1(1));
b = py1(1)-m*px1(1);
lescent_x = mean(cx);
lescent_y = mean(cy);
newb = lescent_y-m*lescent_x;
% comparison is reversed b/c image origin is in a different place than
% cartesian plane.
tibline = sign(newb-b);
if cx(end-1)-cx(1)>cx(end)-cx(1)
cx = cx(1:end-1);
cy = cy(1:end-1);
end
h1 = sqrt((px1(1)-cx(1))^2+(py1(1)-cy(1))^2);
h2 = sqrt((px1(2)-cx(1))^2+(py1(2)-cy(1))^2);
h3 = sqrt((px1(1)-px1(2))^2+(py1(1)-py1(2))^2);
s = (h1+h2+h3)/2;
H = sqrt((4*s*(s-h1)*(s-h2)*(s-h3))/h3^2);
dely = tibline*H*sind(90-theta);
delx = tibline*H*cosd(90-theta);
morey = tibline*round(r/30)*sind(90-theta);
morex = tibline*round(r/30)*cosd(90-theta);
% oldplat = [px1(1) px1(2) py1(1) py1(2)];
px = px1;
py = py1;
px1 = (px(1)-delx)+(tibline)*morex;
px2 = (px(2)-delx)+(tibline)*morex;
py1 = (py(1)+dely)+(tibline*-1)*morey;
py2 = (py(2)+dely)+(tibline*-1)*morey;
% Creating the lesion on the image
Ltemp = zeros(r,c);
for i = 2:size(cx,1)
rpts = linspace(cy(i-1),cy(i),1000); %# A set of row points for the line
cpts = linspace(cx(i-1),cx(i),1000); %# A set of column points for the line
index = sub2ind([r c],round(rpts),round(cpts));
Ltemp(index) = 1;
if i == size(cx,1)
rpts = linspace(cy(1),cy(i),1000); %# A set of row points for the line
cpts = linspace(cx(1),cx(i),1000); %# A set of column points for the line
index = sub2ind([r c],round(rpts),round(cpts));
Ltemp(index) = 1;
end
end
for i = 2:size(ocx,1)
rpts = linspace(ocy(i-1),ocy(i),1000); %# A set of row points for the line
cpts = linspace(ocx(i-1),ocx(i),1000); %# A set of column points for the line
index = sub2ind([r c],round(rpts),round(cpts));
Ltemp(index) = 1;
end
stats = regionprops(Ltemp,'FilledImage','BoundingBox','Centroid','MajorAxisLength','Extrema', 'ConvexArea', 'ConvexHull','ConvexImage','Image','Orientation');
lesion = imrotate(stats.FilledImage,theta);
lesion = imdilate( lesion,strel('square',3));
lesion =imerode(lesion,strel('square',2));
[lesion, lnum] = bwlabel(lesion(:,:,1));
if lnum>1
index = [min(find(sum(lesion==1,1))) min(find(sum(lesion==1,2)))];
target = find(index==max(index));
lesion = lesion(:,min(find(sum(lesion==target,1))):max(find(sum(lesion==target,1))));
[csr, csc] = find(lesion==target);
cart_surf = min(csr);
switch target
case 1
[tmr, tmc] = find(lesion==2);
tidemark = min(tmr);
case 2
[tmr, tmc] = find(lesion==1);
tidemark = min(tmr);
end
lesion = lesion(cart_surf:tidemark,:);
lesion = lesion==target;
else
Ltemp = zeros(r,c);
for i = 2:size(cx,1) % Changed to size(cx,1) from size(cx,2) - DFX
rpts = linspace(cy(i-1),cy(i),1000); %# A set of row points for the line
cpts = linspace(cx(i-1),cx(i),1000); %# A set of column points for the line
index = sub2ind([r c],round(rpts),round(cpts));
Ltemp(index) = 1;
if i == size(cx,2)
rpts = linspace(cy(1),cy(i),1000); %# A set of row points for the line
cpts = linspace(cx(1),cx(i),1000); %# A set of column points for the line
index = sub2ind([r c],round(rpts),round(cpts));
Ltemp(index) = 1;
end
end
stats = regionprops(Ltemp,'FilledImage','BoundingBox','Centroid','MajorAxisLength','Extrema', 'ConvexArea', 'ConvexHull','ConvexImage','Image','Orientation');
lesion = imrotate(stats.FilledImage,theta);
lesion = imdilate( lesion,strel('square',3));
lesion =imerode(lesion,strel('square',2));
[lesion, lnum] = bwlabel(lesion(:,:,1));
lesion = lesion(min(find(sum(lesion,2)>0)):max(find(sum(lesion,2)>0)),:);
end
zstats = regionprops(lesion,'FilledImage','BoundingBox','Centroid','MajorAxisLength','Extrema', 'ConvexArea', 'ConvexHull','ConvexImage','Image','Orientation');
convexles = zstats.ConvexImage;
lesstats = regionprops(convexles, 'Extrema');
extrema = lesstats.Extrema;
perc10 = round(.1*size(lesion,2));
perc90 = round(.9*size(lesion,2));
left = extrema(extrema(:,1)<perc10,:);
left = left(left(:,2)==(min(left(:,2))),:);
if size(left,1)>1
left = left(left(:,1)==(min(left(:,1))),:);
if size(left,1)>1
left = left(1,:);
end
end
right = extrema(extrema(:,1)>perc90,:);
right = right(right(:,2)==(min(right(:,2))),:);
if size(right,1)>1
right = right(right(:,1)==(min(right(:,1))),:);
if size(right,1)>1
right = right(1,:);
end
end
% corrects the rotation angle if the lesion does not quite match
% the tibial plateau angle
alpha = atand((left(2)-right(2))/(left(1)-right(1)));
lesion = imrotate(lesion,.8*alpha);
lesion = lesion(min(find(sum(lesion,2)>0)):end,:); %cut off the blank rows at the top
lesionbrackets = linspace(1,size(lesion,1),12);
lesion0 = lesion(1:max([round(lesionbrackets(2)) round(left(2))+1]),:);
lesion50 = lesion(round(lesionbrackets(6)):round(lesionbrackets(7)),:);
lesion100 = lesion(round(lesionbrackets(11)):end,:);
%two approaches via solid rows and absolute columns:
%widest row of lesion
width0 = max(sum(lesion0,2));
width50 = max(sum(lesion50,2));
width100 = max(sum(lesion100,2));
waitbar(3/10);
%% Cartilage Degeneration Score
lesfill = stats.FilledImage;
Ltemp = zeros(r,c);
Ltemp(round(stats.BoundingBox(2)):round(stats.BoundingBox(2))+size(lesfill,1)-1,...
round(stats.BoundingBox(1)):round(stats.BoundingBox(1))+size(lesfill,2)-1)=lesfill;
rpts = linspace(py1,py2,1000);
cpts = linspace(px1,px2,1000); %# A set of column points for the line
index = sub2ind([r c],round(rpts),round(cpts));
Ltemp(index) = 1;
L = Ltemp;
L = imdilate( L,strel('square',10));
L =imerode(L,strel('square',8));
[L, lnum] = bwlabel(L(:,:,1));
% L = imrotate(L,theta+alpha);
L = imrotate(L,theta);
L = L(min(find(sum(L,2)>0)):max(find(sum(L,2)>0)),min(find(sum(L,1)>0)):max(find(sum(L,1)>0)));
for i = 1:lnum
holdmat=ones(size(L));
holdmat(L(:)~=i)=0;
cstats = regionprops(holdmat,'Centroid','Area','BoundingBox');
Lmat(1,i) = i;
Lmat(2,i) = cstats.Area;
Lmat(3,i) = cstats.Centroid(1);
Lmat(4,i) = cstats.Centroid(2);
Lmat(5,i) = cstats.BoundingBox(1);
Lmat(6,i) = cstats.BoundingBox(2);
Lmat(7,i) = cstats.BoundingBox(3);
Lmat(8,i) = cstats.BoundingBox(4);
end
cartles = Lmat(:,Lmat(7,:)==min(Lmat(7,:)));
L = L==cartles(1);
L = imrotate(L,alpha);
L = L((min(find(sum(L,2)>0))):(max(find(sum(L,2)>0))),:);
zones = linspace(1,size(L,2),4);
zone1 = L(:,round(zones(3)):end);
zone2 = L(:,round(zones(2)):round(zones(3)));
zone3 = L(:,1:round(zones(2)));
CDS(1) = max(sum(zone1,2))/round(zones(2)); ...zone1
CDS(2) = max(sum(zone2,2))/round(zones(2)); ...zone2
CDS(3) = max(sum(zone3,2))/round(zones(2)); ...zone3
for i = 1:3
if CDS(i)<0.05
CDS(i) = 0;
elseif CDS(i)<0.1
CDS(i) = 1;
elseif CDS(i)<0.25
CDS(i) = 2;
elseif CDS(i)<0.5
CDS(i) = 3;
elseif CDS(i)<0.75
CDS(i) = 4;
else
CDS(i) = 5;
end
end
CDSz1 = CDS(1);
CDSz2 = CDS(2);
CDSz3 = CDS(3);
waitbar(4/10);
%% Zonal Depth Ratio
Ltemp(round(stats.BoundingBox(2)):round(stats.BoundingBox(2))+size(lesfill,1)-1,round(stats.BoundingBox(1)):round(stats.BoundingBox(1))+size(lesfill,2)-1)=lesfill;
rpts = linspace(py1,py2,1000); %# A set of row points for the line
cpts = linspace(px1,px2,1000); %# A set of column points for the line
index = sub2ind([r c],round(rpts),round(cpts));
Ltemp(index) = 1;
for i = 2:size(ocx,2)
rpts = linspace(ocy(i-1),ocy(i),1000); %# A set of row points for the line
cpts = linspace(ocx(i-1),ocx(i),1000); %# A set of column points for the line
index = sub2ind([r c],round(rpts),round(cpts));
Ltemp(index) = 1;
end
L = Ltemp;
L = imdilate( L,strel('square',8));
L =imerode(L,strel('square',6));
[L, ~] = bwlabel(L(:,:,1));
L = imrotate(L,theta);
L = L(min(find(sum(L,2)>0)):max(find(sum(L,2)>0)),min(find(sum(L,1)>0)):max(find(sum(L,1)>0)));
L = L(6:end,:);
L = L(min(find(sum(L,2)>0)):max(find(sum(L,2)>0)),min(find(sum(L,1)>0)):max(find(sum(L,1)>0)));
[L, lnum] = bwlabel(L);
zones = linspace(1,size(L,2),7);
zone1 = L(:,round(zones(5)):end);
zone2 = L(:,round(zones(3)):round(zones(5)));
zone3 = L(:,1:round(zones(3)));
center = [zone1(:,round(zones(2))) zone2(:,round(zones(2))) zone3(:,round(zones(2)))];
if lnum==1
for i = 1:3
if sum(center(:,i)==1)>0 % red=2, yellow=1
[holdmat, hnum] = bwlabel(center(:,i));
if hnum>1
redmax = max(find(holdmat==1));
yellowmin = min(find(holdmat==2));
ZDR(1,i) = redmax;
ZDR(2,i) = yellowmin;
ZDR(3,i) = redmax/yellowmin;
else
ZDR(1,i) = 0;
ZDR(2,i) = 0;
ZDR(3,i) = 0;
end
else
ZDR(1,i) = 0;
ZDR(2,i) = 0;
ZDR(3,i) = 0;
end
end
ZDRz1 = ZDR(end,1);
ZDRz2 = ZDR(end,2);
ZDRz3 = ZDR(end,3);
else
for i = 1:3
if sum(center(:,i)==1)>0 && sum(center(:,i)==2)>0 % red=2, yellow=1
redmax = max(find(center(:,i)==2));
yellowmin = min(find(center(:,i)==1));
ZDR(1,i) = redmax;
ZDR(2,i) = yellowmin;
ZDR(3,i) = redmax/yellowmin;
else
ZDR(1,i) = 0;
ZDR(2,i) = 0;
ZDR(3,i) = 0;
end
end
ZDRz1 = ZDR(end,1);
ZDRz2 = ZDR(end,2);
ZDRz3 = ZDR(end,3);
end
else
width0 = 0;
width50 = 0;
width100 = 0;
CDSz1 = 0;
CDSz2 = 0;
CDSz3 = 0;
ZDRz1 = 0;
ZDRz2 = 0;
ZDRz3 = 0;
end
waitbar(5/10);
%% Total and Significant and total Cartilage Degeneration Width
if exist('tcdwx1','var')
if size(tcdwx1)>0
TCDW = sqrt((tcdwx1(1)-tcdwx1(2))^2+(tcdwy1(1)-tcdwy1(2))^2);
else
TCDW = 0;
end
else
TCDW = 0;
end
if exist('scdwx1','var')
if size(scdwx1)>0
SCDW = sqrt((scdwx1(1)-scdwx1(2))^2+(scdwy1(1)-scdwy1(2))^2);
else
SCDW = 0;
end
else
SCDW = 0;
end
waitbar(6/10);
%% 6. Osteophyte
if exist('ostx1','var')
if size(ostx1)>0
OST = sqrt((ostx1(1)-ostx1(2))^2+(osty1(1)-osty1(2))^2);
else
OST = 0;
end
else
OST = 0;
end
waitbar(7/10);
%% 7. Calcified Cartilage and Subchondral bone Damage Score (not included)
%% 8. Synovial Reaction (not included)
%% 9. Medial Joint Capsule Repair and 10. Growth Plate Thickness (both medial and lateral)
SYN = sqrt((sx1(1)-sx1(2))^2+(sy1(1)-sy1(2))^2);
medGP = sqrt((mgpx1(1)-mgpx1(2))^2+(mgpy1(1)-mgpy1(2))^2);
latGP = sqrt((lgpx1(1)-lgpx1(2))^2+(lgpy1(1)-lgpy1(2))^2);
waitbar(8/10);
%% Create master file labels
masterhist{1,1} = 'Sample ID';
masterhist{1,2} = 'Medial Compartment Tibial Plateau Width (pixels)';
masterhist{1,3} = 'Cartilage Matrix Loss Width 0% Lesion Depth (pixels)';... cartilage matrix loss width 0% depth, pixels
masterhist{1,4} = 'Cartilage Matrix Loss Width 50% Lesion Depth (pixels)';... cartilage matrix loss width 50% depth, pixels
masterhist{1,5} = 'Cartilage Matrix Loss Width 1000% Lesion Depth (pixels)';... cartilage matrix loss width 100% depth, pixels
% These are ordinal scores GEKO calculates, but have not been included in
% the final output. Can be included if desired.
% masterhist{1,6} = 'Zone 1 (Medial) Cartilage Degneration Score';... cartilage degeneration score zone1
% masterhist{1,7} = 'Zone 2 (Central) Cartilage Degneration Score';... cartilage degeneration score zone2
% masterhist{1,8} = 'Zone 3 (Lateral) Cartilage Degneration Score';... cartilage degeneration score zone3
masterhist{1,6} = 'Total Cartilage Degneration Width (% of Tibial Plateau)';... total cartilage degeneration width, percentage plateau width
masterhist{1,7} = 'Significant Cartilage Degneration Width (% of Tibial Plateau)';... significant cartilage degeneration width, percentage plateau width
masterhist{1,8} = 'Zone 1 (Medial) Zonal Depth Ratio of Lesion (% Full Cartilage Thickness)';... zonal depth ratio of lesions, zone 1
masterhist{1,9} = 'Zone 2 (Central) Zonal Depth Ratio of Lesion (% Full Cartilage Thickness)';... zonal depth ratio of lesions, zone 2
masterhist{1,10} = 'Zone 3 (Lateral) Zonal Depth Ratio of Lesion (% Full Cartilage Thickness)';... zonal depth ratio of lesions, zone 3
masterhist{1,11} = 'Osteophyte Size (pixels)';... osteophyte length, pixels
masterhist{1,12} = 'Medial Joint Capsule Repair (pixels)';... medial joint capsule repair, pixels
masterhist{1,13} = 'Medial Compartment Medial Growth Plate Thickness (pixels)';... medial growth plate thickness, pixels
masterhist{1,14} = 'Medial Compartment Lateral Growth Plate Thickness (pixels)';... lateral growth plate thickness, pixels
masterhist{1,15} = '# pixel rows in image';
masterhist{1,16} = '# pixel columns in image';
waitbar(9/10);
masterhist{p+1,1} = ID; %'Sample ID';
masterhist{p+1,2} = plateau; %'Medial Compartment Tibial Plateau Width (pixels)';
masterhist{p+1,3} = width0; %'Cartilage Matrix Loss Width 0% Lesion Depth (pixels)';... cartilage matrix loss width 0% depth, pixels
masterhist{p+1,4} = width50; %'Cartilage Matrix Loss Width 50% Lesion Depth (pixels)';... cartilage matrix loss width 50% depth, pixels
masterhist{p+1,5} = width100; %'Cartilage Matrix Loss Width 100% Lesion Depth (pixels)';... cartilage matrix loss width 100% depth, pixels
masterhist{p+1,6} = 100*TCDW/plateau; %'Total Cartilage Degneration Width (% of Tibial Plateau)';... total cartilage degeneration width, percentage plateau width
masterhist{p+1,7} = 100*SCDW/plateau; %'Significant Cartilage Degneration Width (% of Tibial Plateau)';... significant cartilage degeneration width, percentage plateau width
masterhist{p+1,8} = 100*ZDRz1; %'Zone 1 (Medial) Zonal Depth Ratio of Lesion (% Full Cartilage Thickness)';... zonal depth ratio of lesions, zone 1
masterhist{p+1,9} = 100*ZDRz2;%'Zone 2 (Central) Zonal Depth Ratio of Lesion (% Full Cartilage Thickness)';... zonal depth ratio of lesions, zone 2
masterhist{p+1,10} = 100*ZDRz3;%'Zone 3 (Lateral) Zonal Depth Ratio of Lesion (% Full Cartilage Thickness)';... zonal depth ratio of lesions, zone 3
masterhist{p+1,11} = OST; %'Osteophyte Size (pixels)';... osteophyte length, pixels
masterhist{p+1,12} = SYN; %'Medial Joint Capsule Repair (pixels)';... medial joint capsule repail, pixels
masterhist{p+1,13} = medGP; %'Medial Compartment Medial Growth Plate Thickness (pixels)';... medial growth plate thickness, pixels
masterhist{p+1,14} = latGP;%'Medial Compartment Lateral Growth Plate Thickness (pixels)';... lateral growth plate thickness, pixels
masterhist{p+1,15} = r; %'# pixel rows in image';
masterhist{p+1,16} = c; %'# pixel columns in image';
waitbar(10/10);
close(wait);
if length(fname1) == 1
break
end
catch MException
if exist('wait','var') == 1
close(wait);
end
waitfor(msgbox('ERROR encountered, continue to next image.','ERROR','WindowStyle','modal'))
beep
end
end
% Does not try to save if the trial crashed.
if exist('masterhist','var') == 1
% Creates a dialogue box indicated excel sheet is saving. Indicates when
% code is complete. -BYMJ
d = msgbox('Saving data to excel file...','Save','WindowStyle','modal');
set(findobj(d,'style','pushbutton'),'Visible','off')
%% Usable for writing in script format, not in standalone exe -BYMJ
% system('taskkill /F /IM EXCEL.EXE');
% if exist(fullfile(pname1,wfile),'file')
% data = xlsread(fullfile(pname1,wfile));
% % system('taskkill /F /IM EXCEL.EXE');
% [dr, ~] = size(data);
% masterhist = masterhist(2:end,:);
% xlswrite(fullfile(pname1,wfile),masterhist,1,['A' num2str(dr+2)])
% else
% xlswrite(fullfile(pname1,wfile),masterhist,1,'A1')
% end
%% Create spreadsheets in standalone exe -BYMJ
system('taskkill /F /IM EXCEL.EXE');
if exist(fullfile(pname1,wfile),'file')
data = xlsread(fullfile(pname1,wfile));
system('taskkill /F /IM EXCEL.EXE');
[dr, ~] = size(data);
masterhist = table(masterhist(2:end,:));
writetable(masterhist,fullfile(pname1,wfile),'Sheet',1,'Range',['A' num2str(dr+2)],'FileType','spreadsheet')
else
masterhist = table(masterhist);
writetable(masterhist,fullfile(pname1,wfile),'Sheet',1,'Range','A1','FileType','spreadsheet')
end
set(findobj(d,'Tag','MessageBox'),'String','GEKO has finished.')
set(findobj(d,'style','pushbutton'),'Visible','on')
close all
end
function [x,y] = getptsNoDoubleClick(varargin)
%
% This is just a version of getpts that has the stuff that
% handles double clicking turned off because the system
% is so f*#$%ing slow that it thinks single clicks are double
% clicks. End selection by clicking right button. Comments that
% begin with jg show places where the function has been modified.
%
%GETPTS Select points with mouse.
% [X,Y] = GETPTS(FIG) lets you choose a set of points in the
% current axes of figure FIG using the mouse. Coordinates of
% the selected points are returned in the vectors X and Y. Use
% normal button clicks to add points. A shift-, right-, or
% double-click adds a final point and ends the selection.
% Pressing RETURN or ENTER ends the selection without adding
% a final point. Pressing BACKSPACE or DELETE removes the
% previously selected point.
%
% [X,Y] = GETPTS(AX) lets you choose points in the axes
% specified by the handle AX.
%
% [X,Y] = GETPTS is the same as [X,Y] = GETPTS(GCF).
%
% Example
% --------
% imshow('moon.tif')
% [x,y] = getpts
%
% See also GETRECT, GETLINE.
% Callback syntaxes:
% getpts('KeyPress')
% getpts('FirstButtonDown')
% getpts('NextButtonDown')
% Copyright 1993-2004 The MathWorks, Inc.
% $Revision$ $Date$
global GETPTS_FIG GETPTS_AX GETPTS_H1 GETPTS_H2
global GETPTS_PT1
if ((nargin >= 1) && (ischar(varargin{1})))
% Callback invocation: 'KeyPress', 'FirstButtonDown', or
% 'NextButtonDown'.
feval(varargin{:});
return;
end