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vesselness_filter_tool.m
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vesselness_filter_tool.m
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% Vesselness_Filter_Tool
% Script to implement GUI for Vessleness_Filter_Tool. Allows user to load
% an image, select filter parameters, filter the image with a Frangi
% vesselness filter, and save the resulting image.
%
% MPHYGB24: Exercise Sheet #6 (Tasks 2 & 3)
% AUTHOR: Edward James, Medical Imaging CDT MRes , UCL, 2017
function varargout = vesselness_filter_tool(varargin)
% VESSELNESS_FILTER_TOOL MATLAB code for vesselness_filter_tool.fig
% VESSELNESS_FILTER_TOOL, by itself, creates a new VESSELNESS_FILTER_TOOL or raises the existing
% singleton*.
%
% H = VESSELNESS_FILTER_TOOL returns the handle to a new VESSELNESS_FILTER_TOOL or the handle to
% the existing singleton*.
%
% VESSELNESS_FILTER_TOOL('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VESSELNESS_FILTER_TOOL.M with the given input arguments.
%
% VESSELNESS_FILTER_TOOL('Property','Value',...) creates a new VESSELNESS_FILTER_TOOL or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before vesselness_filter_tool_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to vesselness_filter_tool_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help vesselness_filter_tool
% Last Modified by GUIDE v2.5 08-Dec-2017 09:49:13
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @vesselness_filter_tool_OpeningFcn, ...
'gui_OutputFcn', @vesselness_filter_tool_OutputFcn, ...
'gui_LayoutFcn', [], ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before vesselness_filter_tool is made visible.
function vesselness_filter_tool_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to vesselness_filter_tool (see VARARGIN)
%To initialise the GUI sigma and beta values:
start_sigma = 2.7;
start_beta = 0.5;
%To put these values into the edit boxes and slider
set(handles.Sigma_Slider, 'Value', start_sigma);
set(handles.Sigma_EditBox, 'String', num2str(start_sigma));
set(handles.Beta_Editbox, 'String', num2str(start_beta));
% Choose default command line output for vesselness_filter_tool
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes vesselness_filter_tool wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = vesselness_filter_tool_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
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
function Beta_Editbox_Callback(hObject, eventdata, handles)
% hObject handle to Beta_Editbox (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
beta = str2double(get(hObject, 'String')); % get beta value
guidata(hObject, handles); % update handles
% --- Executes during object creation, after setting all properties.
function Beta_Editbox_CreateFcn(hObject, eventdata, handles)
% hObject handle to Beta_Editbox (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
if ispc && isequal(get(hObject, 'BackgroundColor'), get(0, 'defaultUicontrolBackgroundColor'))
set(hObject, 'BackgroundColor', 'white');
end
% --- Executes on button press in Open_Pushbutton.
function Open_Pushbutton_Callback(hObject, eventdata, handles)
% hObject handle to Open_Pushbutton (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Load image.
% File format drop-down box will show .png, .gif, .jpeg, or all file types.
[basefilename, folder] = uigetfile({'*.png'; '*.gif'; '*.jpeg'; '*.*'}, ...
'Select an image to show');
if basefilename == 0
% User has clicked the cancel button or selected a file that does not
% exist, for example
% Display an error message
errordlg('File not found', 'Upload Error', 'modal');
return; % GUI behaves as before (i.e. it will not crash)
end
fullfilename = fullfile(folder, basefilename);
% To catch an error if file selected is not a recognised image type
try
handles.original = imread(fullfilename);
catch
errordlg('File selected is not a recognised image type', ...
'Upload Error', 'modal');
return; % GUI behaves as before (i.e. it will not crash)
end
% Show image in first axes
% axes(handles.axes1);
imshow(handles.original);
% Update handles structure
guidata(hObject, handles);
% --- Executes on button press in Save_Pushbutton.
function Save_Pushbutton_Callback(hObject, eventdata, handles)
% hObject handle to Save_Pushbutton (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%To save filtered image as one of the below types
img = handles.filtered;
[filename, pathname] = uiputfile({'*.png'; '*.gif'; '*.jpeg'; '*.*'}, ...
'Save filtered image as');
if filename == 0
% User has clicked the cancel button, for example.
% Display an error message
errordlg('File not Saved', 'Save Error', 'modal');
return; % GUI behaves as before (i.e. it will not crash)
end
file = fullfile(pathname, filename);
% To catch an error if user attempts to save file as file type that is not
% recognised as an image
try
imwrite(img, file);
catch
errordlg('File not Saved - File format selected is not a recognised image type', ...
'Save Error', 'modal');
return; % GUI behaves as before (i.e. it will not crash)
end
% --- Executes on button press in Filter_Pushbutton.
function Filter_Pushbutton_Callback(hObject, eventdata, handles)
% hObject handle to Filter_Pushbutton (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%Obtain values of beta and sigma
sigma = get(handles.Sigma_EditBox, 'String');
sigma = str2double(sigma);
beta = get(handles.Beta_Editbox, 'String');
beta = str2double(beta);
%Load original image
img = handles.original;
img = im2double(img); % convert image to double precision
img = imcomplement(img); % invert the image intensities
img = vesselness_filter(img, sigma, beta); % filter the image
axes(handles.axes2);
imshow(img); %show image in second axes
%Store and update handles structure.
handles.filtered = img;
guidata(hObject, handles);
% --- Executes on slider movement.
function Sigma_Slider_Callback(hObject, eventdata, handles)
% hObject handle to Sigma_Slider (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
sigma = get(hObject, 'Value'); % returns position of slider
set(handles.Sigma_EditBox, 'String', num2str(sigma)) % update edit box
guidata(hObject, handles) % update handles
% --- Executes during object creation, after setting all properties.
function Sigma_Slider_CreateFcn(hObject, eventdata, handles)
% hObject handle to Sigma_Slider (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: slider controls usually have a light gray background.
if isequal(get(hObject, 'BackgroundColor'), get(0, 'defaultUicontrolBackgroundColor'))
set(hObject, 'BackgroundColor', [.9 .9 .9]);
end
function Sigma_EditBox_Callback(hObject, eventdata, handles)
% hObject handle to Sigma_EditBox (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
sigma = str2double(get(hObject, 'String')); % get value from box
set(handles.Sigma_Slider, 'Value', sigma); % update slider
guidata(hObject, handles); % update handles
% --- Executes during object creation, after setting all properties.
function Sigma_EditBox_CreateFcn(hObject, eventdata, handles)
% hObject handle to Sigma_EditBox (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
if ispc && isequal(get(hObject, 'BackgroundColor'), get(0, 'defaultUicontrolBackgroundColor'))
set(hObject, 'BackgroundColor', 'white');
end
% --- Executes during object creation, after setting all properties.
function figure1_CreateFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% --- Executes during object creation, after setting all properties.
function axes2_CreateFcn(hObject, eventdata, handles)
% hObject handle to axes2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% --- Executes during object creation, after setting all properties.
function axes1_CreateFcn(hObject, eventdata, handles)
% hObject handle to axes1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% --- Executes during object deletion, before destroying properties.
function axes2_DeleteFcn(hObject, eventdata, handles)
% hObject handle to axes2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)