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Fixed bug when 0 artifacts were found
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@sebromano
sebromano authored Nov 16, 2017
1 parent 23c5533 commit c7e28a7
Showing 1 changed file with 105 additions and 104 deletions.
209 changes: 105 additions & 104 deletions Toolbox software/findArtifacts.m
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Original file line number Diff line number Diff line change
Expand Up @@ -230,124 +230,125 @@ function findArtifacts()
DIS_MIN_GR=5;
clear group_mov ind_group_mov
group_mov=1;
ind_group_mov{group_mov}=ind_movements(1);
for i=2:length(ind_movements)
if ind_movements(i)-ind_movements(i-1)<DIS_MIN_GR
ind_group_mov{group_mov}=[ind_group_mov{group_mov} ind_movements(i)];
else
group_mov=group_mov+1;
ind_group_mov{group_mov}=ind_movements(i);
end
end
clean_mov=cell(1,length(ind_group_mov));

dir=0;
windows_frame=5;
hf=figure;
allIn=0;
for quan_mov=1:group_mov
clf
subplot(1,2,1)
posIm=get(gca,'Position');
width=.1; height=.1;
x=posIm(1); y=max(posIm(2)-2*height-0.01,0.01);
uicontrol('Style','pushbutton','String','Pause','CallBack','uiwait(gcf)','Units','normalized','Position',[x y width height]);
x=x+width+0.01;
uicontrol('Style','pushbutton','String','Continue','CallBack','uiresume(gcbf)','Units','normalized','Position',[x y width height]);
x=x+1.5*width;
uicontrol('Style','pushbutton','String','Accept all','CallBack',{@break_function},'Units','normalized','Position',[x y width height]);


x=posIm(1)+posIm(3)+.01; y=posIm(2)+.1;
uicontrol('Style','pushbutton','String','<< Previous frame','CallBack',{@dir_back_function},'Units','normalized','Position',[x y width height]);
x=x+width+0.01;
uicontrol('Style','pushbutton','String','Next frame >>','CallBack',{@dir_foward_function},'Units','normalized','Position',[x y width height]);
x=posIm(1)+posIm(3)+.01; y=y+height+0.01;
uicontrol('Style','pushbutton','String','Yes','CallBack',{@mov_ok_function},'Units','normalized','Position',[x y width height]);
x=x+width+0.01;
uicontrol('Style','pushbutton','String','No','CallBack',{@mov_no_ok_function},'Units','normalized','Position',[x y width height]);


if ind_group_mov{quan_mov}(1)>windows_frame
START=ind_group_mov{quan_mov}(1)-windows_frame;
else
START=1;
end
if ind_group_mov{quan_mov}(end)+windows_frame<numFrames
END=ind_group_mov{quan_mov}(end)+windows_frame;
else
END=numFrames;
if ~isempty(ind_movements)
ind_group_mov{group_mov}=ind_movements(1);
for i=2:length(ind_movements)
if ind_movements(i)-ind_movements(i-1)<DIS_MIN_GR
ind_group_mov{group_mov}=[ind_group_mov{group_mov} ind_movements(i)];
else
group_mov=group_mov+1;
ind_group_mov{group_mov}=ind_movements(i);
end
end
clean_mov=cell(1,length(ind_group_mov));

clear video
video=zeros(END-START,tiffInfo(1).Height,tiffInfo(1).Width, 'single');
for i=START:END
video(i-START+1,:,:)=im2single(imread(fileName,i));
end
video=video(:,rowsRect,colsRect);
video(:,~mask_backup)=0;
width=.2;height=.1;
xTxt=posIm(1)+posIm(3)+.01;yTxt=y+height+.01;
height=.05;
yTxt2=yTxt+height+.01;
while length(clean_mov{quan_mov})~= length(ind_group_mov{quan_mov})
if allIn
break
dir=0;
windows_frame=5;
hf=figure;
allIn=0;
for quan_mov=1:group_mov
clf
subplot(1,2,1)
posIm=get(gca,'Position');
width=.1; height=.1;
x=posIm(1); y=max(posIm(2)-2*height-0.01,0.01);
uicontrol('Style','pushbutton','String','Pause','CallBack','uiwait(gcf)','Units','normalized','Position',[x y width height]);
x=x+width+0.01;
uicontrol('Style','pushbutton','String','Continue','CallBack','uiresume(gcbf)','Units','normalized','Position',[x y width height]);
x=x+1.5*width;
uicontrol('Style','pushbutton','String','Accept all','CallBack',{@break_function},'Units','normalized','Position',[x y width height]);


x=posIm(1)+posIm(3)+.01; y=posIm(2)+.1;
uicontrol('Style','pushbutton','String','<< Previous frame','CallBack',{@dir_back_function},'Units','normalized','Position',[x y width height]);
x=x+width+0.01;
uicontrol('Style','pushbutton','String','Next frame >>','CallBack',{@dir_foward_function},'Units','normalized','Position',[x y width height]);
x=posIm(1)+posIm(3)+.01; y=y+height+0.01;
uicontrol('Style','pushbutton','String','Yes','CallBack',{@mov_ok_function},'Units','normalized','Position',[x y width height]);
x=x+width+0.01;
uicontrol('Style','pushbutton','String','No','CallBack',{@mov_no_ok_function},'Units','normalized','Position',[x y width height]);


if ind_group_mov{quan_mov}(1)>windows_frame
START=ind_group_mov{quan_mov}(1)-windows_frame;
else
START=1;
end
for j=1:length(ind_group_mov{quan_mov})
mov_ok=[];
FRA_TO_SHOW=ind_group_mov{quan_mov}(j)-START+1;
dir=0;
if ind_group_mov{quan_mov}(end)+windows_frame<numFrames
END=ind_group_mov{quan_mov}(end)+windows_frame;
else
END=numFrames;
end

clear video
video=zeros(END-START,tiffInfo(1).Height,tiffInfo(1).Width, 'single');
for i=START:END
video(i-START+1,:,:)=im2single(imread(fileName,i));
end
video=video(:,rowsRect,colsRect);
video(:,~mask_backup)=0;
width=.2;height=.1;
xTxt=posIm(1)+posIm(3)+.01;yTxt=y+height+.01;
height=.05;
yTxt2=yTxt+height+.01;
while length(clean_mov{quan_mov})~= length(ind_group_mov{quan_mov})
if allIn
break
end
while isempty(mov_ok)
for j=1:length(ind_group_mov{quan_mov})
mov_ok=[];
FRA_TO_SHOW=ind_group_mov{quan_mov}(j)-START+1;
dir=0;
if allIn
break
break
end
if (dir==-1 & FRA_TO_SHOW > 1) | (dir==1 & FRA_TO_SHOW < size(video,1))
FRA_TO_SHOW=FRA_TO_SHOW+dir;
while isempty(mov_ok)
if allIn
break
end
if (dir==-1 & FRA_TO_SHOW > 1) | (dir==1 & FRA_TO_SHOW < size(video,1))
FRA_TO_SHOW=FRA_TO_SHOW+dir;
end

dir=0;
subplot(1,2,1)
imagesc(squeeze(video(FRA_TO_SHOW,:,:)))
set(gca,'xticklabel','','ytickLabel','')
axis image
colormap(gray)
caxis([min_video max_video*1.2])
if ismember(START-1+FRA_TO_SHOW, ind_group_mov{quan_mov})
col_frame='r';
else
col_frame='k';
end
title(['Frame number ' num2str(START-1+FRA_TO_SHOW)],'color',col_frame)

uicontrol('Style','text','Units','normalized','position',[xTxt yTxt width height],...
'String',{'Does frame ' num2str(ind_group_mov{quan_mov}(j)) ' contain an artifact?'})

uicontrol('Style','text','Units','normalized','position',[xTxt yTxt2 width height],...
'String',{['Checking frame ' num2str(j) ' (out of ' num2str(length(ind_group_mov{quan_mov})) ')'] ...
['from event ' num2str(quan_mov) ' (out of ' num2str(group_mov) ')']})


drawnow
clean_mov{quan_mov}=[clean_mov{quan_mov} mov_ok];
end

dir=0;
subplot(1,2,1)
imagesc(squeeze(video(FRA_TO_SHOW,:,:)))
set(gca,'xticklabel','','ytickLabel','')
axis image
colormap(gray)
caxis([min_video max_video*1.2])
if ismember(START-1+FRA_TO_SHOW, ind_group_mov{quan_mov})
col_frame='r';
else
col_frame='k';
end
title(['Frame number ' num2str(START-1+FRA_TO_SHOW)],'color',col_frame)

uicontrol('Style','text','Units','normalized','position',[xTxt yTxt width height],...
'String',{'Does frame ' num2str(ind_group_mov{quan_mov}(j)) ' contain an artifact?'})

uicontrol('Style','text','Units','normalized','position',[xTxt yTxt2 width height],...
'String',{['Checking frame ' num2str(j) ' (out of ' num2str(length(ind_group_mov{quan_mov})) ')'] ...
['from event ' num2str(quan_mov) ' (out of ' num2str(group_mov) ')']})


drawnow
clean_mov{quan_mov}=[clean_mov{quan_mov} mov_ok];
end
end
end
end
close(hf)

if allIn
movements=ones(numFrames,1);
else
movements_original=movements;
for quan_mov=1:group_mov
movements(ind_group_mov{quan_mov})=clean_mov{quan_mov};
close(hf)
if allIn
movements=ones(numFrames,1);
else
movements_original=movements;
for quan_mov=1:group_mov
movements(ind_group_mov{quan_mov})=clean_mov{quan_mov};
end
end
end

inputTitle = char('Inform any other artifact');
prompt = {['Are there any other frames that you want to label as artifacts? If so, which ones? (numbers separeted by spaces):']};
answer = inputdlg(prompt, inputTitle, 1);
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