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‎Activeontours/Activeontours/Active Contours implementation & test platform GUI.mlappinstall

1.24 MB
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‎Activeontours/Activeontours/Active Contours implementation & test platform GUI.prj

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<?xml version="1.0" encoding="UTF-8"?>
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<deployment-project plugin="plugin.apptool" plugin-version="1.0">
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<configuration target="target.mlapps" target-name="Package App" name="Active Contours implementation &amp; test platform GUI" location="D:\Kolian\Matlab_scripts\FileExchange\Activeontours" file="D:\Kolian\Matlab_scripts\FileExchange\Activeontours\Active Contours implementation &amp; test platform GUI.prj" build-checksum="1484381674">
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<param.appname>Active Contours implementation &amp; test platform GUI</param.appname>
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<param.authnamewatermark>Nikolay S</param.authnamewatermark>
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<param.email />
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<param.company />
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<param.icon />
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<param.summary>Implementation and demonstration of several active contours segmentation methods.</param.summary>
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<param.description>This program was written as a part of the “Medical Imaging” course. Together with Alex Blekhman (http://www.mathworks.com/matlabcentral/fileexchange/authors/26540)- my partner we have implemented the paper "Active Contours without Edges" by Tony Chan and Luminita Vese. We wrapped it up with a GUI to allow easy parameters change and segmentation process view and results storage for future analysis.
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Later on we have added two existing implementation of additional methods to compare between the methods, and to learn each. The method are:
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1)
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Implementation of "Level Set Evolution Without Re-initialization: A New Variational Formulation" in Proceedings of CVPR'05, vol. 1, pp. 430-436.
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Author: Chunming Li, all rights reserved.
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E-mail: [email protected]
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URL: http://www.engr.uconn.edu/~cmli/
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2)
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Implementation of "Localizing Region Based Active Contours" in “Image Processing, IEEE Transactions on “ im Nov. 2008 by Lankton and Tannenbaum.
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Coded by: Shawn Lankton (www.shawnlankton.com)
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This is the place to thank both authors for the code contribution.
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The users who download this code are welcome to play with it, to try and learn the above segmentation schemes. Moreover, additional methods can be added, and the GUI may serve as a convenient platform for segmentation methods understanding, analysis and comparisons.
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Best segmenting you all!</param.description>
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<param.screenshot>D:\Kolian\Matlab_scripts\FileExchange\preview.jpg</param.screenshot>
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<param.version>1.0</param.version>
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<param.products.name>
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<item>MATLAB</item>
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<item>Signal Processing Toolbox</item>
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<item>Image Processing Toolbox</item>
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<item>Statistics Toolbox</item>
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</param.products.name>
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<param.products.id>
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<item>1</item>
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<item>8</item>
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<item>17</item>
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<item>19</item>
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</param.products.id>
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<param.products.version>
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<item>8.0</item>
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<item>6.18</item>
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<item>8.1</item>
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<item>8.1</item>
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</param.products.version>
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<param.platforms />
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<param.output>${PROJECT_ROOT}\Active Contours implementation &amp; test platform GUI.mlappinstall</param.output>
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<param.guid>e78c8aa2-ba65-436c-805a-b05619730ae5</param.guid>
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<unset>
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<param.email />
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<param.company />
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<param.icon />
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<param.version />
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<param.platforms />
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</unset>
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<fileset.main>
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<file>${PROJECT_ROOT}\ActiveCountorsGUI.m</file>
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</fileset.main>
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<fileset.depfun>
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<file>${PROJECT_ROOT}\ActiveContoursWihoutEdges.m</file>
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<file>${PROJECT_ROOT}\ActiveCountorsGUI.fig</file>
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<file>${PROJECT_ROOT}\Images\128X128\BallsClusters.jpg</file>
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<file>${PROJECT_ROOT}\Images\128X128\BallsClustersLightBalls.jpg</file>
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<file>${PROJECT_ROOT}\Images\128X128\Shapes.JPG</file>
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<file>${PROJECT_ROOT}\Images\128X128\Thumbs.db</file>
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<file>${PROJECT_ROOT}\Images\256X256\BallsClusters.jpg</file>
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<file>${PROJECT_ROOT}\Images\256X256\BallsClustersLightBalls.jpg</file>
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<file>${PROJECT_ROOT}\Images\256X256\BallsOnGray.jpg</file>
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<file>${PROJECT_ROOT}\Images\256X256\BlurredBallsOnGray.jpg</file>
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<file>${PROJECT_ROOT}\Images\256X256\BlurredShapesOnGray1.jpg</file>
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<file>${PROJECT_ROOT}\Images\256X256\BlurredShapesOnGray2.jpg</file>
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<file>${PROJECT_ROOT}\Images\256X256\monkey.png</file>
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<file>${PROJECT_ROOT}\Images\256X256\PaperSpiral.jpg</file>
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<file>${PROJECT_ROOT}\Images\256X256\Thumbs.db</file>
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<file>${PROJECT_ROOT}\Images\64X64\BallsClusters.jpg</file>
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<file>${PROJECT_ROOT}\Images\64X64\Brodats1.tiff</file>
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<file>${PROJECT_ROOT}\Images\64X64\Brodats2.tiff</file>
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<file>${PROJECT_ROOT}\Images\64X64\Egypt8.tif</file>
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<file>${PROJECT_ROOT}\Images\64X64\Egypt9.tif</file>
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<file>${PROJECT_ROOT}\Images\64X64\EuropeNight1.jpg</file>
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<file>${PROJECT_ROOT}\Images\64X64\EuropeNight2.jpg</file>
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<file>${PROJECT_ROOT}\Images\64X64\GradientBall.jpg</file>
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<file>${PROJECT_ROOT}\Images\64X64\HiResSpiral.jpg</file>
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<file>${PROJECT_ROOT}\Images\64X64\Lena.jpg</file>
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<file>${PROJECT_ROOT}\Images\64X64\LenaText.jpg</file>
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<file>${PROJECT_ROOT}\Images\64X64\LinesSketch.jpg</file>
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<file>${PROJECT_ROOT}\Images\64X64\monkey.png</file>
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<file>${PROJECT_ROOT}\Images\64X64\PaperSpiral.jpg</file>
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<file>${PROJECT_ROOT}\Images\64X64\ShapesOnGray1.jpg</file>
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<file>${PROJECT_ROOT}\Images\64X64\ShapesOnGray2.jpg</file>
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<file>${PROJECT_ROOT}\Images\64X64\twocells.bmp</file>
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<file>${PROJECT_ROOT}\Images\64X64\twoObj.bmp</file>
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<file>${PROJECT_ROOT}\InfoFiles\ActiveContoursAbout.htm</file>
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<file>${PROJECT_ROOT}\InfoFiles\ActiveContoursHelp.htm</file>
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<file>${PROJECT_ROOT}\LevelSetEvolutionWithoutReinitialization.m</file>
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<file>${PROJECT_ROOT}\localized_seg.m</file>
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</fileset.depfun>
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<fileset.resources>
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<file>${PROJECT_ROOT}\Images</file>
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<file>${PROJECT_ROOT}\InfoFiles</file>
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</fileset.resources>
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<fileset.package />
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<build-deliverables>
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<file name="Active Contours implementation &amp; test platform GUI.mlappinstall" location="D:\Kolian\Matlab_scripts\FileExchange\Activeontours" optional="false">D:\Kolian\Matlab_scripts\FileExchange\Activeontours\Active Contours implementation &amp; test platform GUI.mlappinstall</file>
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</build-deliverables>
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<workflow />
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<matlab>
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<root>C:\Program Files\MATLAB\R2012b</root>
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</matlab>
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<platform>
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<unix>false</unix>
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<mac>false</mac>
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<windows>true</windows>
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<win2k>false</win2k>
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<winxp>false</winxp>
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<vista>false</vista>
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<linux>false</linux>
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<solaris>false</solaris>
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<osver>6.1</osver>
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<os32>false</os32>
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<os64>true</os64>
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<arch>win64</arch>
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<matlab>true</matlab>
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</platform>
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</configuration>
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</deployment-project>
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‎Activeontours/Activeontours/ActiveContoursWihoutEdges.m

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function ActiveContoursWihoutEdges(hObject,mask)
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%This function implements the paper "Active Contours without Edges" by
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%Tony Chan and Luminita Vese. It also present results accourding to user
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%wish (from ActiveCountorsGUI). Coding- Nikolay S. & Alex B.
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%Input argument- a Handle to an object of ActiveCountorsGUI
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handles=guidata(hObject);
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%% get Alg parametrs from GUI
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N=get(handles.NAlgEdit,'Value'); % number of iterations
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Lambda_1=get(handles.Lambda1AlgEdit,'Value');
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Lambda_2=get(handles.Lambda2AlgEdit,'Value');
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miu=get(handles.MiuAlgEdit,'Value'); % varies from 255*1e-1 to 255*1e-4
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v=get(handles.NuAlgEdit,'Value');
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delta_t=get(handles.DeltaTAlgEdit,'Value');
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HTflag=get(handles.HTBasedAlg,'Value');
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%% Get visual/plotting parameters
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FigRefresRate=get(handles.RefreshRateEdit,'Value');
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SaveRefresRate=get(handles.SaveRateEdit,'Value');
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SegDispaly=get(handles.SegmentOn,'Value');
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EnergyDispaly=get(handles.EnergyOn,'Value');
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EnergyImageType=get(handles.EnergyPlotTypeMenu,'Value');
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no_of_plots=SegDispaly+EnergyDispaly;
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uipael_handle=handles.Axis_uipanel;
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if no_of_plots==1
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%set(handles.GUIfig,'CurrentAxes',handles.Axes)
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subplot(no_of_plots,1,1,'Units','Normalized','Parent',uipael_handle)
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end
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%% get I/O parameters
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out_dir=handles.OutDirPath;
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% get file name from path
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file_str=handles.ImageFileAddr;
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% [pathstr, name, ext, versn] = fileparts(filename)
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[~, in_file_name, ~] = fileparts(file_str);
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text_line_length=60;
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%% divide name too long to cell array to allow compact presentation in text command
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length_file_str=length(file_str);
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cell_array_length=ceil(length_file_str/text_line_length);
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file_str4text=cell(1,cell_array_length);
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for ind=1:cell_array_length-1
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file_str4text{ind}=[file_str((1+(ind-1)*text_line_length):...
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ind*text_line_length),'...'];
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end
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file_str4text{ind+1}=file_str((1+ind*text_line_length):end);
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%% load image
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img=handles.ImageData;
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[img_x,img_y]=size(img);
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%% Init Phi
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phi=bwdist(1-mask)-bwdist(mask);
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% phi=phi.^3;
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phi=phi/(max(max(phi))-min(min(phi))); %normilize to amplitude=1
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% K=zeros(img_x,img_y); %init K matrix
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if ~strcmpi(class(phi),'double')
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phi=double(phi);
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end
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%define HT
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if (HTflag)
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% x=-i*sign(linspace(0,1,150)-.5);
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N_U=10;N_V=10;
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[U,V]=meshgrid(linspace(-fix(N_U/2),fix(N_U/2),N_U),linspace(-fix(N_V/2),fix(N_V/2),N_U));
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H_UV_HT=sign(U).*sign(V);
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h_ht=fftshift(ifft(H_UV_HT));
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end
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for n=1:N % main loop
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%% Active contours iterations
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c_1=sum(img(phi>=0))/max(1,length(img(phi>0))); % prevent division by zero
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c_2=sum(img(phi<0))/max(1,length(img(phi<0))); % prevent division by zero
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if (HTflag)
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dx=filter2(h_ht,phi,'same');
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dy=dx.';
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else
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[dx,dy]=gradient(phi);
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end
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grad_norm=max(eps,sqrt(dx.^2+dy.^2));%we want to prevent division by zero
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% [dxx,dxy]=gradient(dx);
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% [dyx,dyy]=gradient(dy);
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% K=(dxx.*dy.^2-2*dx.*dy.*dxy+dyy.*dx.^2)./(grad_norm).^3; % another way to define div(grad/|grad|)
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K=divergence(dx./grad_norm,dy./grad_norm); %this one is a bit faster
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speed = Delta_eps(phi).*(miu*K-v-Lambda_1*(img-c_1).^2+Lambda_2*(img-c_2).^2);
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speed =speed/ sqrt(sum(sum(speed.^2)));%norm by square root of sum of square elements
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phi=phi+delta_t*speed;
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%% Presenting relevant graphs
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if (~mod(n,FigRefresRate)) % it's time to draw current image
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pause(0.001);
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if (SegDispaly)
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if (EnergyDispaly) % two axis on display
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subplot(no_of_plots,1,1,'Units','Normalized',...
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'Parent',uipael_handle);
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end
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% imshow(uint8(repmat(img,[1,1,3])));hold on;
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strechedImg=img-min(img(:)); % now values are between 0:Max
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strechedImg=255*strechedImg/max(strechedImg(:)); % now values between 0:255
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imshow(repmat(uint8(strechedImg),[1,1,3]),[]); hold on;
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contour(sign(phi),[0 0],'g','LineWidth',2);
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iterNum=['Segmentation with: Active Contours wihtout Edges, ',num2str(n),' iterations'];
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title(iterNum,'FontSize',14);
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axis off;axis equal;hold off;
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end
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if (EnergyDispaly)
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if (SegDispaly) % two axis on display
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subplot(no_of_plots,1,2,'Units','Normalized',...
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'Parent',uipael_handle)
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end
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switch(EnergyImageType)
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case(1) %surf(phi)
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surf(phi);
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case(2) %mesh(phi)
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mesh(phi);
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case(3) %imagesc(phi)
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imagesc(phi);
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axis equal;
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axis off;
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case(4) %surf(sign|phi|)
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surf(sign(phi));
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case(5) %mesh(sign|phi|)
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mesh(sign(phi));
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case(6) %imagesc(sign|phi|);
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imagesc(sign(phi));
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axis equal;axis off;
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end
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colormap('Jet');
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title(['\phi_{',num2str(n),'}'],'FontSize',18);
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end
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if (SegDispaly)&&(EnergyDispaly)
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text_pos=[0.5,1.35];
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else
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text_pos=[0.5,-0.02];
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end
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text(text_pos(1),text_pos(2),{'Applied to file:',file_str4text{:}},...
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'HorizontalAlignment','center','Units','Normalized',...
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'FontUnits','Normalized');
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drawnow;
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%% it's time to save current image
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if (~mod(n,SaveRefresRate))
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tmp=zeros(size(img,1),size(img,2));
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tmp(phi>0)=255;
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temp_img=repmat(img(:,:,1),[1 1 3]);
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temp_img(:,:,2)=temp_img(:,:,2)+tmp;
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imwrite(uint8(temp_img),[out_dir,filesep,in_file_name,'Segment_n_',num2str(n),'.jpg'],'jpg');
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max_phi=max(max(phi));min_phi=min(min(phi));
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tmp=phi; tmp=255*(tmp-min_phi)/(max_phi-min_phi);
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imwrite(uint8(tmp),[out_dir,filesep,in_file_name,'Phi_n_',num2str(n),'.jpg'],'jpg');
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% saveas(gca,[out_dir,filesep,num2str(n)],'fig') ;%save figure
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end % if (~mod(n,SaveRefresRate))
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end % if (~mod(n,FigRefresRate))
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end % for n=1:N % main loop
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% Servise sub function %
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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function out=Delta_eps(z,epsilon)
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if nargin==1
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epsilon=1;
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end
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out=epsilon/pi./(epsilon^2+z.^2);
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% out=(1/(2*epsilon))*(1+cos(pi*z/epsilon)).*(abs(z)<=epsilon);

‎Activeontours/Activeontours/ActiveCountorsGUI.fig

28.7 KB
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