├── LICENSE ├── README.md ├── _config.yml ├── curvilinear_gui.fig ├── curvilinear_gui.m ├── include ├── gaussgradient │ ├── README.txt.txt │ ├── gaussgradient.m │ └── testgaussgradient.m ├── hysterisis │ ├── hysteresis3d.m │ └── license.txt ├── imoverlay │ ├── imoverlay.m │ └── license.txt └── vessel_center_line_detector.m └── screenshot.png /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | 676 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Curveliniar_Detector 2 | Curveliniar structures extraxtor. Center lines, blood vessels etc.. 3 | 4 | ![screenshot](/screenshot.png) 5 | 6 | # References 7 | [1] Guanglei Xiong (xgl99@mails.tsinghua.edu.cn) at Tsinghua University, Beijing, China. [Gradient using first order derivative of Gaussian](http://www.mathworks.com/matlabcentral/fileexchange/8060-gradient-using-first-order-derivative-of-gaussian/content/gaussgradient/gaussgradient.m) 8 | 9 | [2] Luke Xie, 2013 [Hysteresis thresholding for 3D images (or 2D)](http://www.mathworks.com/matlabcentral/fileexchange/44648-hysteresis-thresholding-for-3d-images--or-2d-/content/hysteresis3d.m) 10 | 11 | [3] The MathWorks, Inc., 2012 [Image overlay](http://www.mathworks.com/matlabcentral/fileexchange/10502-image-overlay/content/imoverlay.m) 12 | 13 | [4] [J.J. Staal, M.D. Abramoff, M. Niemeijer, M.A. Viergever, B. van Ginneken, "Ridge based vessel segmentation in color images of the retina", IEEE Transactions on Medical Imaging, 2004, vol. 23, pp. 501-509.](http://www.isi.uu.nl/Research/Publications/publicationview.php?id=855) 14 | 15 | [5] C. Steger, “An Unbiased Detector of Curvilinear Structures”, IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, VOL. 20, NO. 2, pp. 113 – 125, FEBRUARY 1998. -------------------------------------------------------------------------------- /_config.yml: -------------------------------------------------------------------------------- 1 | theme: jekyll-theme-slate -------------------------------------------------------------------------------- /curvilinear_gui.fig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kapcom01/Curviliniar_Detector/b435151f1082d01ed28207a9c4fd5ccfa3b019c5/curvilinear_gui.fig -------------------------------------------------------------------------------- /curvilinear_gui.m: -------------------------------------------------------------------------------- 1 | function varargout = curvilinear_gui(varargin) 2 | % CURVILINEAR MATLAB code for CURVILINEAR.fig 3 | % CURVILINEAR, by itself, creates a new CURVILINEAR or raises the existing 4 | % singleton*. 5 | 6 | % Edit the above text to modify the response to help CURVILINEAR 7 | 8 | % Last Modified by GUIDE v2.5 13-Jul-2015 18:42:36 9 | 10 | % Begin initialization code - DO NOT EDIT 11 | gui_Singleton = 1; 12 | gui_State = struct('gui_Name', mfilename, ... 13 | 'gui_Singleton', gui_Singleton, ... 14 | 'gui_OpeningFcn', @curvilinear_OpeningFcn, ... 15 | 'gui_OutputFcn', @curvilinear_OutputFcn, ... 16 | 'gui_LayoutFcn', [] , ... 17 | 'gui_Callback', []); 18 | if nargin && ischar(varargin{1}) 19 | gui_State.gui_Callback = str2func(varargin{1}); 20 | end 21 | 22 | if nargout 23 | [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); 24 | else 25 | gui_mainfcn(gui_State, varargin{:}); 26 | end 27 | % End initialization code - DO NOT EDIT 28 | 29 | 30 | % --- Executes just before CURVILINEAR is made visible. 31 | function curvilinear_OpeningFcn(hObject, eventdata, handles, varargin) 32 | % This function has no output args, see OutputFcn. 33 | % hObject handle to figure 34 | % eventdata reserved - to be defined in a future version of MATLAB 35 | % handles structure with handles and user data (see GUIDATA) 36 | % varargin command line arguments to CURVILINEAR (see VARARGIN) 37 | 38 | % Choose default command line output for CURVILINEAR 39 | handles.output = hObject; 40 | 41 | addpath('include/'); 42 | addpath('include/imoverlay/'); 43 | addpath('include/gaussgradient/'); 44 | addpath('include/hysterisis/'); 45 | 46 | % setup global vars 47 | refresh_gaussian_graph(handles, 1); 48 | handles.overlay_color=[0 1 0]; 49 | handles.line_type = -1; 50 | 51 | % Update handles structure 52 | guidata(hObject, handles); 53 | 54 | 55 | % --- Outputs from this function are returned to the command line. 56 | function varargout = curvilinear_OutputFcn(hObject, eventdata, handles) 57 | % varargout cell array for returning output args (see VARARGOUT); 58 | % hObject handle to figure 59 | % eventdata reserved - to be defined in a future version of MATLAB 60 | % handles structure with handles and user data (see GUIDATA) 61 | 62 | % Get default command line output from handles structure 63 | varargout{1} = handles.output; 64 | 65 | 66 | % --- Executes on button press in pb_open. 67 | function pb_open_Callback(hObject, eventdata, handles) 68 | % hObject handle to pb_open (see GCBO) 69 | % eventdata reserved - to be defined in a future version of MATLAB 70 | % handles structure with handles and user data (see GUIDATA) 71 | [filename, pathname] = uigetfile( ... 72 | {'*.jpg;*.png;*.bmp;*.tif',... 73 | 'Images (*.jpg,*.png,*.bmp,*.tif)'; 74 | '*.*', 'All Files (*.*)'}, ... 75 | 'Select Image'); 76 | if filename == 0 77 | return; 78 | end 79 | axes(handles.axes1); 80 | imshow(imread([pathname filename])); 81 | 82 | update_output_image(handles); 83 | 84 | 85 | % --- Executes on button press in pb_save. 86 | function pb_save_Callback(hObject, eventdata, handles) 87 | % hObject handle to pb_save (see GCBO) 88 | % eventdata reserved - to be defined in a future version of MATLAB 89 | % handles structure with handles and user data (see GUIDATA) 90 | [filename, pathname] = uiputfile( ... 91 | {'*.jpg;*.png;*.bmp;*.tif',... 92 | 'Images (*.jpg,*.png,*.bmp,*.tif)'; 93 | '*.*', 'All Files (*.*)'}, ... 94 | 'Select Folder'); 95 | if filename == 0 96 | return; 97 | end 98 | A = getimage(handles.axes2); 99 | B = getimage(handles.axes3); 100 | imwrite(A,[pathname 'binary_' filename]); 101 | imwrite(B,[pathname 'overlay_' filename]); 102 | 103 | 104 | function edit_lower_Callback(hObject, eventdata, handles) 105 | % hObject handle to edit_lower (see GCBO) 106 | % eventdata reserved - to be defined in a future version of MATLAB 107 | % handles structure with handles and user data (see GUIDATA) 108 | 109 | % Hints: get(hObject,'String') returns contents of edit_lower as text 110 | % str2double(get(hObject,'String')) returns contents of edit_lower as a double 111 | if strcmp(eventdata.Key, 'return') 112 | set(handles.slider2, 'Value', str2num(get(hObject,'String'))); 113 | update_output_image(handles); 114 | end 115 | 116 | 117 | % --- Executes during object creation, after setting all properties. 118 | function edit_lower_CreateFcn(hObject, eventdata, handles) 119 | % hObject handle to edit_lower (see GCBO) 120 | % eventdata reserved - to be defined in a future version of MATLAB 121 | % handles empty - handles not created until after all CreateFcns called 122 | 123 | % Hint: edit controls usually have a white background on Windows. 124 | % See ISPC and COMPUTER. 125 | if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) 126 | set(hObject,'BackgroundColor','white'); 127 | end 128 | 129 | 130 | % --- Executes on button press in checkbox3. 131 | function checkbox3_Callback(hObject, eventdata, handles) 132 | % hObject handle to checkbox3 (see GCBO) 133 | % eventdata reserved - to be defined in a future version of MATLAB 134 | % handles structure with handles and user data (see GUIDATA) 135 | 136 | % Hint: get(hObject,'Value') returns toggle state of checkbox3 137 | 138 | 139 | % --- Executes on slider movement. 140 | function slider1_Callback(hObject, eventdata, handles) 141 | % hObject handle to slider1 (see GCBO) 142 | % eventdata reserved - to be defined in a future version of MATLAB 143 | % handles structure with handles and user data (see GUIDATA) 144 | 145 | % Hints: get(hObject,'Value') returns position of slider 146 | % get(hObject,'Min') and get(hObject,'Max') to determine range of slider 147 | set(handles.edit_upper, 'String', get(hObject, 'Value')); 148 | update_output_image(handles); 149 | 150 | % --- Executes during object creation, after setting all properties. 151 | function slider1_CreateFcn(hObject, eventdata, handles) 152 | % hObject handle to slider1 (see GCBO) 153 | % eventdata reserved - to be defined in a future version of MATLAB 154 | % handles empty - handles not created until after all CreateFcns called 155 | 156 | % Hint: slider controls usually have a light gray background. 157 | if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) 158 | set(hObject,'BackgroundColor',[.9 .9 .9]); 159 | end 160 | 161 | % --- Executes during object creation, after setting all properties. 162 | function slider2_CreateFcn(hObject, eventdata, handles) 163 | % hObject handle to slider2 (see GCBO) 164 | % eventdata reserved - to be defined in a future version of MATLAB 165 | % handles empty - handles not created until after all CreateFcns called 166 | 167 | % Hint: slider controls usually have a light gray background. 168 | if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) 169 | set(hObject,'BackgroundColor',[.9 .9 .9]); 170 | end 171 | 172 | 173 | % --- Executes on slider movement. 174 | function slider2_Callback(hObject, eventdata, handles) 175 | % hObject handle to slider2 (see GCBO) 176 | % eventdata reserved - to be defined in a future version of MATLAB 177 | % handles structure with handles and user data (see GUIDATA) 178 | 179 | % Hints: get(hObject,'Value') returns position of slider 180 | % get(hObject,'Min') and get(hObject,'Max') to determine range of slider 181 | set(handles.edit_lower, 'String', get(hObject, 'Value')); 182 | update_output_image(handles); 183 | 184 | 185 | function edit_upper_Callback(hObject, eventdata, handles) 186 | % hObject handle to edit_upper (see GCBO) 187 | % eventdata reserved - to be defined in a future version of MATLAB 188 | % handles structure with handles and user data (see GUIDATA) 189 | 190 | % Hints: get(hObject,'String') returns contents of edit_upper as text 191 | % str2double(get(hObject,'String')) returns contents of edit_upper as a double 192 | if strcmp(eventdata.Key, 'return') 193 | set(handles.slider1, 'Value', str2num(get(hObject,'String'))); 194 | update_output_image(handles); 195 | end 196 | 197 | 198 | % --- Executes during object creation, after setting all properties. 199 | function edit_upper_CreateFcn(hObject, eventdata, handles) 200 | % hObject handle to edit_upper (see GCBO) 201 | % eventdata reserved - to be defined in a future version of MATLAB 202 | % handles empty - handles not created until after all CreateFcns called 203 | 204 | % Hint: edit controls usually have a white background on Windows. 205 | % See ISPC and COMPUTER. 206 | if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) 207 | set(hObject,'BackgroundColor','white'); 208 | end 209 | 210 | 211 | function edit_sigma_Callback(hObject, eventdata, handles) 212 | % hObject handle to edit_sigma (see GCBO) 213 | % eventdata reserved - to be defined in a future version of MATLAB 214 | % handles structure with handles and user data (see GUIDATA) 215 | 216 | % Hints: get(hObject,'String') returns contents of edit_sigma as text 217 | % str2double(get(hObject,'String')) returns contents of edit_sigma as a double 218 | 219 | 220 | % --- Executes during object creation, after setting all properties. 221 | function edit_sigma_CreateFcn(hObject, eventdata, handles) 222 | % hObject handle to edit_sigma (see GCBO) 223 | % eventdata reserved - to be defined in a future version of MATLAB 224 | % handles empty - handles not created until after all CreateFcns called 225 | 226 | % Hint: edit controls usually have a white background on Windows. 227 | % See ISPC and COMPUTER. 228 | if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) 229 | set(hObject,'BackgroundColor','white'); 230 | end 231 | 232 | 233 | % --- Executes on slider movement. 234 | function slider_sigma_Callback(hObject, eventdata, handles) 235 | % hObject handle to slider_sigma (see GCBO) 236 | % eventdata reserved - to be defined in a future version of MATLAB 237 | % handles structure with handles and user data (see GUIDATA) 238 | 239 | % Hints: get(hObject,'Value') returns position of slider 240 | % get(hObject,'Min') and get(hObject,'Max') to determine range of slider 241 | set(handles.edit_sigma, 'String', get(hObject, 'Value')); 242 | update_output_image(handles); 243 | 244 | % --- Executes during object creation, after setting all properties. 245 | function slider_sigma_CreateFcn(hObject, eventdata, handles) 246 | % hObject handle to slider_sigma (see GCBO) 247 | % eventdata reserved - to be defined in a future version of MATLAB 248 | % handles empty - handles not created until after all CreateFcns called 249 | 250 | % Hint: slider controls usually have a light gray background. 251 | if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) 252 | set(hObject,'BackgroundColor',[.9 .9 .9]); 253 | end 254 | 255 | 256 | % --- Executes on key press with focus on edit_sigma and none of its controls. 257 | function edit_sigma_KeyPressFcn(hObject, eventdata, handles) 258 | % hObject handle to edit_sigma (see GCBO) 259 | % eventdata structure with the following fields (see UICONTROL) 260 | % Key: name of the key that was pressed, in lower case 261 | % Character: character interpretation of the key(s) that was pressed 262 | % Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed 263 | % handles structure with handles and user data (see GUIDATA) 264 | if strcmp(eventdata.Key, 'return') 265 | set(handles.slider_sigma, 'Value', str2num(get(hObject,'String'))); 266 | update_output_image(handles); 267 | end 268 | 269 | 270 | % --- Executes when selected object is changed in panel_line_types. 271 | function panel_line_types_SelectionChangeFcn(hObject, eventdata, handles) 272 | % hObject handle to the selected object in panel_line_types 273 | % eventdata structure with the following fields (see UIBUTTONGROUP) 274 | % EventName: string 'SelectionChanged' (read only) 275 | % OldValue: handle of the previously selected object or empty if none was selected 276 | % NewValue: handle of the currently selected object 277 | % handles structure with handles and user data (see GUIDATA) 278 | handles.line_type=get(eventdata.NewValue, 'UserData'); 279 | guidata(hObject, handles); 280 | update_output_image(handles); 281 | 282 | % --- Executes when selected object is changed in panel_overlay_colors. 283 | function panel_overlay_colors_SelectionChangeFcn(hObject, eventdata, handles) 284 | % hObject handle to the selected object in panel_overlay_colors 285 | % eventdata structure with the following fields (see UIBUTTONGROUP) 286 | % EventName: string 'SelectionChanged' (read only) 287 | % OldValue: handle of the previously selected object or empty if none was selected 288 | % NewValue: handle of the currently selected object 289 | % handles structure with handles and user data (see GUIDATA) 290 | handles.overlay_color=get(eventdata.NewValue, 'BackgroundColor'); 291 | guidata(hObject, handles); 292 | update_output_image(handles); 293 | 294 | function refresh_sliders(handles,min,max) 295 | if get(handles.slider1, 'Max')>max 296 | set(handles.slider1, 'Value', max); 297 | end 298 | if get(handles.slider2, 'Max')>max 299 | set(handles.slider2, 'Value', max); 300 | end 301 | if get(handles.slider1, 'Min')0 335 | minlamda=0; 336 | maxlamda=max(max(lamda)); 337 | elseif line_type == 1 338 | % bright lines in dark background 339 | % lamda must be <0 340 | maxlamda=0; 341 | minlamda=min(min(lamda)); 342 | elseif line_type == 0 343 | % both type of lines 344 | end 345 | refresh_sliders(handles,minlamda,maxlamda); 346 | 347 | t1=get(handles.slider1,'Value'); 348 | t2=get(handles.slider2,'Value'); 349 | [tri,hys]=hysteresis3d(lamda,t1,t2,8); 350 | 351 | axes(handles.axes2); 352 | imshow(hys); 353 | axes(handles.axes3); 354 | imshow(imoverlay(inputImage, hys, handles.overlay_color)); 355 | -------------------------------------------------------------------------------- /include/gaussgradient/README.txt.txt: -------------------------------------------------------------------------------- 1 | GAUSSGRADIENT Gradient using first order derivative of Gaussian. 2 | [gx,gy]=gaussgradient(IM,sigma) outputs the gradient image gx and gy of 3 | image IM using a 2-D Gaussian kernel. Sigma is the standard deviation of 4 | this kernel along both directions. 5 | 6 | Contributed by Guanglei Xiong (xgl99@mails.tsinghua.edu.cn) 7 | at Tsinghua University, Beijing, China. 8 | 9 | Please try testgrassgradient.m first! -------------------------------------------------------------------------------- /include/gaussgradient/gaussgradient.m: -------------------------------------------------------------------------------- 1 | function [gx,gy]=gaussgradient(IM,sigma) 2 | %GAUSSGRADIENT Gradient using first order derivative of Gaussian. 3 | % [gx,gy]=gaussgradient(IM,sigma) outputs the gradient image gx and gy of 4 | % image IM using a 2-D Gaussian kernel. Sigma is the standard deviation of 5 | % this kernel along both directions. 6 | % 7 | % Contributed by Guanglei Xiong (xgl99@mails.tsinghua.edu.cn) 8 | % at Tsinghua University, Beijing, China. 9 | 10 | %determine the appropriate size of kernel. The smaller epsilon, the larger 11 | %size. 12 | epsilon=1e-2; 13 | halfsize=ceil(sigma*sqrt(-2*log(sqrt(2*pi)*sigma*epsilon))); 14 | size=2*halfsize+1; 15 | %generate a 2-D Gaussian kernel along x direction 16 | for i=1:size 17 | for j=1:size 18 | u=[i-halfsize-1 j-halfsize-1]; 19 | hx(i,j)=gauss(u(1),sigma)*dgauss(u(2),sigma); 20 | end 21 | end 22 | hx=hx/sqrt(sum(sum(abs(hx).*abs(hx)))); 23 | %generate a 2-D Gaussian kernel along y direction 24 | hy=hx'; 25 | % surf(hx) 26 | %2-D filtering 27 | gx=imfilter(IM,hx,'replicate','conv'); 28 | gy=imfilter(IM,hy,'replicate','conv'); 29 | 30 | function y = gauss(x,sigma) 31 | %Gaussian 32 | y = exp(-x^2/(2*sigma^2)) / (sigma*sqrt(2*pi)); 33 | 34 | function y = dgauss(x,sigma) 35 | %first order derivative of Gaussian 36 | y = -x * gauss(x,sigma) / sigma^2; -------------------------------------------------------------------------------- /include/gaussgradient/testgaussgradient.m: -------------------------------------------------------------------------------- 1 | clear;close all; 2 | im=imread('rice.png'); 3 | fim=mat2gray(im); 4 | %draw magnitude of gradient 5 | figure('name','Magnitude of Gradient'); 6 | [imx,imy]=gaussgradient(fim,0.5); 7 | subplot(2,2,1); imshow(abs(imx)+abs(imy)); title('sigma=0.5'); 8 | [imx,imy]=gaussgradient(fim,1.0); 9 | subplot(2,2,2); imshow(abs(imx)+abs(imy)); title('sigma=1.0'); 10 | [imx,imy]=gaussgradient(fim,1.5); 11 | subplot(2,2,3); imshow(abs(imx)+abs(imy)); title('sigma=1.5'); 12 | [imx,imy]=gaussgradient(fim,2.0); 13 | subplot(2,2,4); imshow(abs(imx)+abs(imy)); title('sigma=2.0'); 14 | 15 | %draw gradeint in a small region with sigma=1.0 16 | [imx,imy]=gaussgradient(fim,1.0); 17 | figure('name','Gradient'); 18 | imshow(fim(1:50,1:50),'InitialMagnification','fit'); 19 | hold on; 20 | quiver(imx(1:50,1:50),imy(1:50,1:50)); 21 | title('sigma=1.0'); -------------------------------------------------------------------------------- /include/hysterisis/hysteresis3d.m: -------------------------------------------------------------------------------- 1 | function [tri,hys]=hysteresis3d(img,t1,t2,conn) 2 | % function [tri,hys]=HYSTERESIS3D(img,t1,t2,conn) 3 | % 4 | % Hysteresis3d is a simple function that performs trinarisation and 5 | % hysteresis for 2D and 3D images. Hysteresis3d was inspired by Peter 6 | % Kovesi's 2D hysteresis function 7 | % (http://www.csse.uwa.edu.au/~pk/research/matlabfns/). This 3D function 8 | % takes advantage of the 3D connectivities of imfill instead of the 2D 9 | % connectivities of bwselect. 10 | % 11 | % Usage: [tri,hys]=HYSTERESIS3D(img,t1,t2,conn) 12 | % 13 | % Arguments: img - image for hysteresis (assumed to be non-negative) 14 | % t1 - lower threshold value (fraction b/w 0-1, e.g.: 0.1) 15 | % t2 - upper threshold value (fraction b/w 0-1, e.g.: 0.9) 16 | % (t1/t2 can be entered in any order, larger one will be 17 | % set as the upper threshold) 18 | % conn - number of connectivities (4 or 8 for 2D) 19 | % (6, 18, or 26 for 3D) 20 | % Returns: 21 | % tri - the trinarisation image (values are 0, 1, or 2) 22 | % hys - the hysteresis image (logical mask image) 23 | % 24 | % Examples: [tri,hys]=HYSTERESIS3D(img,0.25,0.8,26) 25 | % 26 | % 2012/07/10: written by Luke Xie 27 | % 2013/12/09: defaults added 28 | % 29 | % To see an example of hysteresis used to segment a kidney region, please 30 | % refer to supplement in QSM of Kidney, NMR Biomed, 2013 Dec;26(12):1853-63 31 | % (http://onlinelibrary.wiley.com/doi/10.1002/nbm.3039/abstract). 32 | % Supplemental material is also available on our CIVMspace: 33 | % http://www.civm.duhs.duke.edu/lx201204/ 34 | 35 | %% arguments 36 | if nargin<3 37 | disp('function needs at least 3 inputs') 38 | return; 39 | elseif nargin==3 40 | disp('inputs=3') 41 | if numel(size(img))==2; 42 | disp('img=2D') 43 | disp('conn set at 4 connectivies (number of neighbors)') 44 | conn=4; 45 | end 46 | if numel(size(img))==3; 47 | disp('img=3D') 48 | disp('conn set at 6 connectivies (number of neighbors)') 49 | conn=6; 50 | end 51 | end 52 | 53 | %% scale t1 & t2 based on image intensity range 54 | if t1>t2 % swap values if t1>t2 55 | tmp=t1; 56 | t1=t2; 57 | t2=tmp; 58 | end 59 | minv=min(img(:)); % min image intensity value 60 | maxv=max(img(:)); % max image intensity value 61 | t1v=t1*(maxv-minv)+minv; 62 | t2v=t2*(maxv-minv)+minv; 63 | 64 | %% trinarisation 65 | tri=zeros(size(img)); 66 | tri(img>=t1v)=1; 67 | tri(img>=t2v)=2; 68 | 69 | %% hysteresis 70 | abovet1=img>t1v; % points above lower threshold 71 | seed_indices=sub2ind(size(abovet1),find(img>t2v)); % indices of points above upper threshold 72 | hys=imfill(~abovet1,seed_indices,conn); % obtain all connected regions in abovet1 that include points with values above t2 73 | hys=hys & abovet1; 74 | 75 | -------------------------------------------------------------------------------- /include/hysterisis/license.txt: -------------------------------------------------------------------------------- 1 | Copyright (c) 2013, Luke Xie 2 | All rights reserved. 3 | 4 | Redistribution and use in source and binary forms, with or without 5 | modification, are permitted provided that the following conditions are 6 | met: 7 | 8 | * Redistributions of source code must retain the above copyright 9 | notice, this list of conditions and the following disclaimer. 10 | * Redistributions in binary form must reproduce the above copyright 11 | notice, this list of conditions and the following disclaimer in 12 | the documentation and/or other materials provided with the distribution 13 | * Neither the name of the nor the names 14 | of its contributors may be used to endorse or promote products derived 15 | from this software without specific prior written permission. 16 | 17 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 18 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 19 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 20 | ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 21 | LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 22 | CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 23 | SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 24 | INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 25 | CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 26 | ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 27 | POSSIBILITY OF SUCH DAMAGE. 28 | -------------------------------------------------------------------------------- /include/imoverlay/imoverlay.m: -------------------------------------------------------------------------------- 1 | function out = imoverlay(in, mask, color) 2 | %IMOVERLAY Create a mask-based image overlay. 3 | % OUT = IMOVERLAY(IN, MASK, COLOR) takes an input image, IN, and a binary 4 | % image, MASK, and produces an output image whose pixels in the MASK 5 | % locations have the specified COLOR. 6 | % 7 | % IN should be a grayscale or an RGB image of class uint8, uint16, int16, 8 | % logical, double, or single. If IN is double or single, it should be in 9 | % the range [0, 1]. If it is not in that range, you might want to use 10 | % mat2gray to scale it into that range. 11 | % 12 | % MASK should be a two-dimensional logical matrix. 13 | % 14 | % COLOR should be a 1-by-3 vector of values in the range [0, 1]. [0 0 0] 15 | % is black, and [1 1 1] is white. 16 | % 17 | % OUT is a uint8 RGB image. 18 | % 19 | % Examples 20 | % -------- 21 | % Overlay edge detection result in green over the original image. 22 | % 23 | % I = imread('cameraman.tif'); 24 | % bw = edge(I, 'canny'); 25 | % rgb = imoverlay(I, bw, [0 1 0]); 26 | % imshow(rgb) 27 | % 28 | % Treating the output of peaks as an image, overlay the values greater than 29 | % 7 in red. The output of peaks is not in the usual grayscale image range 30 | % of [0, 1], so use mat2gray to scale it. 31 | % 32 | % I = peaks; 33 | % mask = I > 7; 34 | % rgb = imoverlay(mat2gray(I), mask, [1 0 0]); 35 | % imshow(rgb, 'InitialMagnification', 'fit') 36 | 37 | % Steven L. Eddins 38 | % Copyright 2006-2012 The MathWorks, Inc. 39 | 40 | % If the user doesn't specify the color, use white. 41 | DEFAULT_COLOR = [1 1 1]; 42 | if nargin < 3 43 | color = DEFAULT_COLOR; 44 | end 45 | 46 | % Force the 2nd input to be logical. 47 | mask = (mask ~= 0); 48 | 49 | % Make the uint8 the working data class. The output is also uint8. 50 | in_uint8 = im2uint8(in); 51 | color_uint8 = im2uint8(color); 52 | 53 | % Initialize the red, green, and blue output channels. 54 | if ndims(in_uint8) == 2 55 | % Input is grayscale. Initialize all output channels the same. 56 | out_red = in_uint8; 57 | out_green = in_uint8; 58 | out_blue = in_uint8; 59 | else 60 | % Input is RGB truecolor. 61 | out_red = in_uint8(:,:,1); 62 | out_green = in_uint8(:,:,2); 63 | out_blue = in_uint8(:,:,3); 64 | end 65 | 66 | % Replace output channel values in the mask locations with the appropriate 67 | % color value. 68 | out_red(mask) = color_uint8(1); 69 | out_green(mask) = color_uint8(2); 70 | out_blue(mask) = color_uint8(3); 71 | 72 | % Form an RGB truecolor image by concatenating the channel matrices along 73 | % the third dimension. 74 | out = cat(3, out_red, out_green, out_blue); 75 | -------------------------------------------------------------------------------- /include/imoverlay/license.txt: -------------------------------------------------------------------------------- 1 | Copyright (c) 2012, The MathWorks, Inc. 2 | All rights reserved. 3 | 4 | Redistribution and use in source and binary forms, with or without 5 | modification, are permitted provided that the following conditions are 6 | met: 7 | 8 | * Redistributions of source code must retain the above copyright 9 | notice, this list of conditions and the following disclaimer. 10 | * Redistributions in binary form must reproduce the above copyright 11 | notice, this list of conditions and the following disclaimer in 12 | the documentation and/or other materials provided with the distribution 13 | * Neither the name of the The MathWorks, Inc. nor the names 14 | of its contributors may be used to endorse or promote products derived 15 | from this software without specific prior written permission. 16 | 17 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 18 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 19 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 20 | ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 21 | LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 22 | CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 23 | SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 24 | INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 25 | CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 26 | ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 27 | POSSIBILITY OF SUCH DAMAGE. 28 | -------------------------------------------------------------------------------- /include/vessel_center_line_detector.m: -------------------------------------------------------------------------------- 1 | function [lamdam] = vessel_center_line_detector(Image,s,line_type) 2 | % function [lamdam] = vessel_center_line_detector(Image,s) 3 | % 4 | % Detects center lines (blood vessels) 5 | % 6 | % 7 | % Arguments: Image - Input Image 8 | % s - sigma value for gaussian filter 9 | % line_type - -1 for dark lines in light background 10 | % 1 for bright lines in dark background 11 | % 0 for both type of lines 12 | % 13 | % Returns: lamdam - the eigenvalues that belong to perpendicular 14 | % eigenvectors with zero gradient. 15 | % 16 | % 17 | 18 | 19 | % open image, convert to gray scale 20 | I=im2double(rgb2gray(Image)); 21 | 22 | % % create gaussian kernel (s=sigma) 23 | % g = fspecial('gaussian', [15 15], s); 24 | 25 | % % 1st and 2nd order Gaussian Gradients 26 | % [gx, gy] = gradient(g); 27 | % [g2x, g2xy] = gradient(gx); 28 | % [g2xy, g2y] = gradient(gy); 29 | 30 | % % 1st and second order Image Gradients(convolution with gaussian 31 | % % gradients) 32 | % Ix=(s^2)*conv2(double(I),gx,'same'); 33 | % Iy=(s^2)*conv2(double(I),gy,'same'); 34 | % Ixx=(s^2)*conv2(double(I),g2x,'same'); 35 | % Iyy=(s^2)*conv2(double(I),g2y,'same'); 36 | % Ixy=conv2(double(I),g2xy,'same'); 37 | 38 | [Ix,Iy]=gaussgradient(I,s); 39 | [Ixx,Ixy]=gaussgradient(Ix,s); 40 | [Ixy,Iyy]=gaussgradient(Iy,s); 41 | 42 | % Calculate max eigenvalues (lamdam) of Hessian matrix [Ixx Ixy; Ixy Iyy] 43 | a=Ixx;b=Ixy;c=Iyy; 44 | q=0.5*((a+c)+sign(a+c).*sqrt((a-c).^2+4*b.^2)); 45 | lamda1=q; 46 | lamda2=(a.*c-b.^2)./q; 47 | lamdam=max(lamda1,lamda2); 48 | 49 | % Calculate eigenvectors (umx,umy) of lamdam 50 | umx=abs(b)./sqrt(b.^2+(lamdam-a).^2); 51 | umy=sign(b).*(lamdam-a)./sqrt(b.^2+(lamdam-a).^2); 52 | 53 | t=-(umx.*Ix+umy.*Iy)./(umx.^2.*Ixx+2*umx.*umy.*Ixy+umy.^2.*Iyy); 54 | 55 | for y=1:size(umx,2) 56 | for x=1:size(umx,1) 57 | tumx=t(x,y)*umx(x,y); 58 | tumy=t(x,y)*umy(x,y); 59 | % if eigenvectors not perpendicular to center line 60 | if lamdam(x,y)*line_type>0 || (abs(tumx)>0.5 || abs(tumy)>0.5) 61 | % then dismiss this eigenvalue 62 | % by setting an invalid value 63 | lamdam(x,y)=line_type; 64 | end 65 | end 66 | end 67 | -------------------------------------------------------------------------------- /screenshot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kapcom01/Curviliniar_Detector/b435151f1082d01ed28207a9c4fd5ccfa3b019c5/screenshot.png --------------------------------------------------------------------------------