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Merge branch 'master' of https://github.com/neuropoly/axon_segmentation
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Aldo Zaimi committed Sep 21, 2016
2 parents ae085d6 + dfd20e6 commit c93c6b7
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Showing 6 changed files with 150 additions and 129 deletions.
Binary file modified code/GUI/ManualCorrectionGUI.fig
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236 changes: 126 additions & 110 deletions code/GUI/ManualCorrectionGUI.m
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Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,10 @@
%
% path_img = uigetimagefile;
% img_BW_test = imread(path_img);
%
%
% path_ctrl = uigetimagefile;
% img_BW_control = imread(path_ctrl);
%
%
% ManualCorrectionGUI(path_img,path_ctrl);
%
%--------------------------------------------------------------------------
Expand Down Expand Up @@ -40,11 +40,11 @@
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @ManualCorrectionGUI_OpeningFcn, ...
'gui_OutputFcn', @ManualCorrectionGUI_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @ManualCorrectionGUI_OpeningFcn, ...
'gui_OutputFcn', @ManualCorrectionGUI_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
Expand All @@ -70,23 +70,39 @@ function ManualCorrectionGUI_OpeningFcn(hObject, eventdata, handles, varargin)
handles.output = hObject;

% Input 1 expected to be the image
if length(varargin)<1, [varargin{1}, PathName]=uigetfile({'*.jpg;*.tif;*.png;*.gif','All Image Files';'*.nii;*.nii.gz','NIFTI files'}); varargin{1} = [PathName, varargin{1}]; end
if strfind(varargin{1},'.nii')
handles.img = load_nii_data(varargin{1});
else
handles.img = imread(varargin{1});
handles.img = rgb2gray(imread(varargin{1}));
end

% Image is enhanced to help manual segmentation
handles.img=adapthisteq(handles.img);

% Input 2 expected to be initial binary mask
handles.axsegfname=varargin{2};
if strfind(handles.axsegfname,'.nii')
handles.bw_axonseg = load_nii_data(handles.axsegfname);
if length(varargin)>1,
handles.axsegfname=varargin{2};


if strfind(handles.axsegfname,'.nii')
handles.bw_axonseg = load_nii_data(handles.axsegfname);
else
handles.bw_axonseg = imread(handles.axsegfname);
end
else
handles.bw_axonseg = imread(handles.axsegfname);
[path, filename, ext]=fileparts(varargin{1});
handles.axsegfname = [path, filename, '_ManualSeg', ext];
handles.bw_axonseg = false(size(handles.img));
end

% Initialize variables:
handles.length_y = size(handles.img,1);
handles.length_x = size(handles.img,2);
handles.current_mask = handles.bw_axonseg;
handles.current_img = handles.img;
handles.mask_position = [1 handles.length_y 1 handles.length_x];

% Display image and initial mask on GUI
axes(handles.axes1);
sc(get(handles.alpha,'Value')*sc(handles.bw_axonseg,'y',handles.bw_axonseg)+sc(handles.img));
Expand All @@ -103,7 +119,7 @@ function ManualCorrectionGUI_OpeningFcn(hObject, eventdata, handles, varargin)


% --- Outputs from this function are returned to the command line.
function varargout = ManualCorrectionGUI_OutputFcn(hObject, eventdata, handles)
function varargout = ManualCorrectionGUI_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
Expand Down Expand Up @@ -163,81 +179,81 @@ function add_Callback(hObject, eventdata, handles)
try

if get(handles.freehand,'Value')==1
roi_free=imfreehand;
roi_free=imfreehand;
elseif get(handles.polygon,'Value')==1
roi_free=impoly;
% elseif get(handles.ellipse,'Value')==1
% roi_free=imellipse;
roi_free=impoly;
% elseif get(handles.ellipse,'Value')==1
% roi_free=imellipse;
end

coords=roi_free.getPosition;

%%

% if isfield(handles, 'current_mask')
% if isfield(handles, 'current_mask')

% binary mask of the new axon in zoomed image
bw_added=poly2mask(coords(:,1),coords(:,2),size(handles.current_mask,1),size(handles.current_mask,2));

% else
%
% bw=poly2mask(coords(:,1),coords(:,2),size(handles.bw_axonseg,1),size(handles.bw_axonseg,2));
%
% end
% else
%
% bw=poly2mask(coords(:,1),coords(:,2),size(handles.bw_axonseg,1),size(handles.bw_axonseg,2));
%
% end

%%
roi_free.delete
catch err
break
end


% bw_empty=zeros(size(handles.bw_axonseg,1),size(handles.bw_axonseg,2));

% if handles.zoom_value==1
% bw=bw_zoom;
% else

% if isfield(handles, 'current_mask')
% bw(handles.mask_position(1):handles.mask_position(2),handles.mask_position(3):handles.mask_position(4))=bw_zoom;
% end

% end

%
% bw_zoom=bw_zoom|bw_added;

% handles.before_add=handles.bw_axonseg(handles.mask_position(1):handles.mask_position(2),handles.mask_position(3):handles.mask_position(4));

handles.bw_axonseg(handles.mask_position(1):handles.mask_position(2),handles.mask_position(3):handles.mask_position(4))=...
handles.bw_axonseg(handles.mask_position(1):handles.mask_position(2),handles.mask_position(3):handles.mask_position(4))|bw_added;

% handles.bw_axonseg=handles.bw_axonseg | bw;


% alpha_Callback(hObject, eventdata, handles)

guidata(hObject, handles);

if isfield(handles, 'current_mask')

length_y=handles.length_y;
length_x=handles.length_x;

display_img=handles.img(get(handles.slider_x,'Value')+1:get(handles.slider_x,'Value')+length_y,get(handles.slider_y,'Value')+1:get(handles.slider_y,'Value')+length_x);
display_mask=handles.bw_axonseg(get(handles.slider_x,'Value')+1:get(handles.slider_x,'Value')+length_y,get(handles.slider_y,'Value')+1:get(handles.slider_y,'Value')+length_x);
sc(get(handles.alpha,'Value')*sc(display_mask,'y',display_mask)+sc(display_img));

else

display_img=handles.img;
display_mask=handles.bw_axonseg;
sc(get(handles.alpha,'Value')*sc(display_mask,'y',display_mask)+sc(display_img));

end



% bw_empty=zeros(size(handles.bw_axonseg,1),size(handles.bw_axonseg,2));

% if handles.zoom_value==1
% bw=bw_zoom;
% else

% if isfield(handles, 'current_mask')
% bw(handles.mask_position(1):handles.mask_position(2),handles.mask_position(3):handles.mask_position(4))=bw_zoom;
% end

% end

%
% bw_zoom=bw_zoom|bw_added;

% handles.before_add=handles.bw_axonseg(handles.mask_position(1):handles.mask_position(2),handles.mask_position(3):handles.mask_position(4));

handles.bw_axonseg(handles.mask_position(1):handles.mask_position(2),handles.mask_position(3):handles.mask_position(4))=...
handles.bw_axonseg(handles.mask_position(1):handles.mask_position(2),handles.mask_position(3):handles.mask_position(4))|bw_added;

% handles.bw_axonseg=handles.bw_axonseg | bw;


% alpha_Callback(hObject, eventdata, handles)

guidata(hObject, handles);

if isfield(handles, 'current_mask')

length_y=handles.length_y;
length_x=handles.length_x;

display_img=handles.img(get(handles.slider_x,'Value')+1:get(handles.slider_x,'Value')+length_y,get(handles.slider_y,'Value')+1:get(handles.slider_y,'Value')+length_x);
display_mask=handles.bw_axonseg(get(handles.slider_x,'Value')+1:get(handles.slider_x,'Value')+length_y,get(handles.slider_y,'Value')+1:get(handles.slider_y,'Value')+length_x);
sc(get(handles.alpha,'Value')*sc(display_mask,'y',display_mask)+sc(display_img));

else

display_img=handles.img;
display_mask=handles.bw_axonseg;
sc(get(handles.alpha,'Value')*sc(display_mask,'y',display_mask)+sc(display_img));

end



end
set(handles.add,'Value',0)

Expand All @@ -250,10 +266,10 @@ function remove_Callback(hObject, eventdata, handles)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
uiresume
BW2=bwmorph(handles.bw_axonseg,'shrink',3);
sc(handles.img,'r',BW2);
BW2=bwmorph(handles.bw_axonseg(handles.mask_position(1):handles.mask_position(2),handles.mask_position(3):handles.mask_position(4)),'shrink',3);
sc(handles.img(get(handles.slider_x,'Value')+1:get(handles.slider_x,'Value')+handles.length_y,get(handles.slider_y,'Value')+1:get(handles.slider_y,'Value')+handles.length_x),'r',BW2);
try
handles.bw_axonseg=as_obj_remove(handles.bw_axonseg);
handles.bw_axonseg(handles.mask_position(1):handles.mask_position(2),handles.mask_position(3):handles.mask_position(4))=as_obj_remove(handles.bw_axonseg(handles.mask_position(1):handles.mask_position(2),handles.mask_position(3):handles.mask_position(4)));
end
alpha_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
Expand Down Expand Up @@ -288,23 +304,23 @@ function show_grid_Callback(hObject, eventdata, handles)
% handles structure with handles and user data (see GUIDATA)

if get(handles.show_grid,'Value')==1
grid_size=3;
grid_size=3;
grid_row=round(length(handles.img2(:,1))/grid_size);
grid_col=round(length(handles.img2(1,:))/grid_size);
handles.img2(grid_row:grid_row:end,:,:)=255;
handles.img2(:,grid_col:grid_col:end,:)=255;
handles.img2(grid_row:grid_row:end,:,:)=255;
handles.img2(:,grid_col:grid_col:end,:)=255;
sc(get(handles.alpha,'Value')*sc(handles.bw_axonseg,'copper')+sc(handles.img2))
end
guidata(hObject, handles);


%
% if handles.Grid ==1
% grid_size = 3;
%
% if handles.Grid ==1
% grid_size = 3;
% grid_row = round(length(handles.img2(:,1))/grid_size);
% grid_col = round(length(handles.img2(1,:))/grid_size);
% handles.img2(grid_row:grid_row:end,:,:) = 255; %# creat 3x3 grid over image to facilitate segmentation process
% handles.img2(:,grid_col:grid_col:end,:) = 255;
% handles.img2(:,grid_col:grid_col:end,:) = 255;
% sc(get(handles.alpha,'Value')*sc(handles.bw_axonseg,'copper')+sc(handles.img2))
% else
% grid_size = 1;
Expand Down Expand Up @@ -348,11 +364,11 @@ function zoom_scale_Callback(hObject, eventdata, handles)

handles.length_x=length_x;
handles.length_y=length_y;
%

%
% display_img=handles.img(1:round(end/zoom_val),1:round(end/zoom_val));
% display_mask=handles.bw_axonseg(1:round(end/zoom_val),1:round(end/zoom_val));
%
%


% sc(get(handles.alpha,'Value')*sc(display_mask,'copper')+sc(display_img));
Expand All @@ -362,32 +378,32 @@ function zoom_scale_Callback(hObject, eventdata, handles)


if zoom_val>1

set(handles.slider_x, 'Visible','on');
set(handles.slider_y, 'Visible','on');
set(handles.text3, 'Visible','on');
set(handles.text4, 'Visible','on');

set(handles.slider_x,'Max',size(handles.img,1)-length_y);
set(handles.slider_x, 'SliderStep', [1/(size(handles.img,1)-length_y) , 20/(size(handles.img,1)-length_y) ]);
set(handles.slider_x,'Value',0);

set(handles.slider_y,'Max',size(handles.img,2)-length_x);
set(handles.slider_y, 'SliderStep', [1/(size(handles.img,2)-length_x) , 20/(size(handles.img,2)-length_x) ]);
set(handles.slider_y,'Value',0);

update_display(hObject, eventdata, handles);

set(handles.slider_x, 'Visible','on');
set(handles.slider_y, 'Visible','on');
set(handles.text3, 'Visible','on');
set(handles.text4, 'Visible','on');
set(handles.slider_x,'Max',size(handles.img,1)-length_y);
set(handles.slider_x, 'SliderStep', [1/(size(handles.img,1)-length_y) , 20/(size(handles.img,1)-length_y) ]);
set(handles.slider_x,'Value',0);
set(handles.slider_y,'Max',size(handles.img,2)-length_x);
set(handles.slider_y, 'SliderStep', [1/(size(handles.img,2)-length_x) , 20/(size(handles.img,2)-length_x) ]);
set(handles.slider_y,'Value',0);
update_display(hObject, eventdata, handles);
else

set(handles.slider_x, 'Visible','off');
set(handles.slider_y, 'Visible','off');
set(handles.text3, 'Visible','off');
set(handles.text4, 'Visible','off');
set(handles.slider_x, 'Visible','off');
set(handles.slider_y, 'Visible','off');
set(handles.text3, 'Visible','off');
set(handles.text4, 'Visible','off');

display_img=handles.img;
display_mask=handles.bw_axonseg;
sc(get(handles.alpha,'Value')*sc(display_mask,'y',display_mask)+sc(display_img));
display_img=handles.img;
display_mask=handles.bw_axonseg;
sc(get(handles.alpha,'Value')*sc(display_mask,'y',display_mask)+sc(display_img));

end

Expand Down Expand Up @@ -505,18 +521,18 @@ function region_growing_Callback(hObject, eventdata, handles)

I = im2double(handles.current_img);

[y,x]=getpts;
y=round(y);
[y,x]=getpts;
y=round(y);
x=round(x);

if size(x)==1
J = regiongrowing(I,x,y);
J = as_regiongrowing(I,x,y);
else
J = regiongrowing(I,x(1),y(1));
J = as_regiongrowing(I,x(1),y(1));

for i=2:size(x,1)

J_i = regiongrowing(I,x(i),y(i));
J_i = as_regiongrowing(I,x(i),y(i));

J = J|J_i;
end
Expand Down
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