2D/3D image segmentation toolbox

2D/3D image segmentation using level-set based active contour/surface with AOS scheme

Description

 Features of the toolbox:
(1) The toolbox includes classic level-set methods such as geodesic active contours (GAC), Chan-Vese model and a hybrid model combining the boundary and regional terms.
(2) All the methods are implemented with the semi-implicit solver AOS which can guarantee the stability of the numerical methods even with very large time steps, thus boosting the efficiency for level-set based segmentation.
(3) All the methods can be applied to 2D and 3D data.

• Required Products: Image Processing Toolbox
• MATLAB release: MATLAB 7.2 (R2006a)
• Other Files: AOSLevelsetSegmentationToolboxM.rar, ; license.txt

[jichao zhao]

It seems quite cool, but when I compiled mex, and I met some errors. Do not know how to fix it.

[Sebastien Paris]

Works fine.

[Yan Zhang]

Hi Jichao, can you tell me which compiler you are using and provide more information about the errors?

[Jackson Shen]

Exellent Work. *****

[jichao zhao]

Hi, Zhang Yan. Yes when I used compile_mex_codes to compile, I met the following errors:

BinaryHeap.h: In member function 'void CBinaryHeapMinSort<IndexType, WeightType>::Insert(IndexType, WeightType) [with IndexType = int, WeightType = double]':
ac_distance_transform_3d.cpp:25: instantiated from 'void DistanceTransform3D(const InputType*, OutputType*, const int*) [with InputType = unsigned char, OutputType = double]'
ac_distance_transform_3d.cpp:106: instantiated from here
BinaryHeap.h:50: error: no matching function for call to 'std::exception::exception(const char [30])'
/usr/include/c++/4.2/exception:59: note: candidates are: std::exception::exception()
/usr/include/c++/4.2/exception:57: note: std::exception::exception(const std::exception&)

    mex: compile of 'ac_distance_transform_3d.cpp' failed.

Thanks for any hint so that I can fix it and use your package, cheers, jichao

[Yan Zhang]

Hi, Jichao. To fix the problem:
(1) Open BinaryHeap.h in the "mex" folder
(2) Locate "std::exception" in the file
(3) Get rid of the string "CFastMarching: Heap overflow!" (It works fine for MSVC, but for GCC std::exception class doesn't accept argument for its constructor.)
(4) Run compile_all_codes.m.

Please don't hesitate to contact me if there are any further questions.

[Ahmed]

i downloaded the pre-compiled version and it worked, the thing is the documentation is not enough for me and i don't quite understand the different variables used and the inputs too

[Ning]

Hi Yan, i am new to the mex feature, could you tell me how to install your toolbox?
Thx!

[Yan Zhang]

Hi, Ning. Please read the 'readme.txt' file in the package, all the essential messages are there. Basically, (1) unzip the package and open matlab (2) in the matlab environment, go to the 'mex' folder and run 'compile_mex_codes', all the mex files will be automatically compiled and moved to the right directory. If this is your first time using the mex function, make sure to use 'mex -setup' command in the matlab command window to select an appropriate c++ compiler (MSVC, GCC or whatever).

[Ning]

Hi Yan,thx for the quick reply. I followed the instruction, but when i tried to run the compile_mex_codes, it can not get through, i attached the msg it gave out, could you tell me how to solve this? Thx again.

 lcc preprocessor warning: ac_tridiagonal_Thomas_dll.cpp:95 No newline at end of file
Error ac_tridiagonal_Thomas_dll.cpp: 7 syntax error; found `unsigned' expecting `;'
Error ac_tridiagonal_Thomas_dll.cpp: 7 syntax error; found `unsigned' expecting `;'
Error ac_tridiagonal_Thomas_dll.cpp: 7 syntax error; found `unsigned' expecting `)'
Error ac_tridiagonal_Thomas_dll.cpp: 7 skipping `unsigned' `long' `int'
Error ac_tridiagonal_Thomas_dll.cpp: 7 undeclared identifier `i'
Warning ac_tridiagonal_Thomas_dll.cpp: 7 Statement has no effect
Warning ac_tridiagonal_Thomas_dll.cpp: 7 unreachable code
Error ac_tridiagonal_Thomas_dll.cpp: 7 syntax error; found `)' expecting `;'
Error ac_tridiagonal_Thomas_dll.cpp: 7 illegal statement termination
Error ac_tridiagonal_Thomas_dll.cpp: 7 skipping `)'
Error ac_tridiagonal_Thomas_dll.cpp: 19 undeclared identifier `new'
Error ac_tridiagonal_Thomas_dll.cpp: 19 operands of = have illegal types `pointer to double' and `int'
Warning ac_tridiagonal_Thomas_dll.cpp: 19 possible usage of new before definition
Error ac_tridiagonal_Thomas_dll.cpp: 19 syntax error; found `double' expecting `;'
Error ac_tridiagonal_Thomas_dll.cpp: 19 integer expression must be constant
Error ac_tridiagonal_Thomas_dll.cpp: 19 missing identifier
Error ac_tridiagonal_Thomas_dll.cpp: 51 undeclared identifier `delete'
Error ac_tridiagonal_Thomas_dll.cpp: 51 illegal expression
Error ac_tridiagonal_Thomas_dll.cpp: 51 syntax error; found `yy' expecting `]'
Error ac_tridiagonal_Thomas_dll.cpp: 51 type error: pointer expected
Warning ac_tridiagonal_Thomas_dll.cpp: 51 Statement has no effect
Error ac_tridiagonal_Thomas_dll.cpp: 51 syntax error; found `yy' expecting `;'
Warning ac_tridiagonal_Thomas_dll.cpp: 51 Statement has no effect
Warning ac_tridiagonal_Thomas_dll.cpp: 51 possible usage of delete before definition
Error ac_tridiagonal_Thomas_dll.cpp: 71 illegal statement termination
Error ac_tridiagonal_Thomas_dll.cpp: 71 skipping `double'
Error ac_tridiagonal_Thomas_dll.cpp: 71 too many errors
 
  C:\PROGRAM FILES\MATLAB\R2006A\BIN\MEX.PL: Error: Compile of 'ac_tridiagonal_Thomas_dll.cpp' failed.

[Yan Zhang]

Hi, Ning. Can you tell me which compiler are you using? It looks to me that the compiler doesn't support C++ (can't recognize keywords 'new', 'delete' and operator overloads). If you are using gcc, make sure link to the standard c++ library using '-lstdc++' or directly use g++.

If you are using Windows system, a more complete version of the toolbox can be downloaded from the following link:
http://ecson.org/resources/software/_AOSLevelsetSegmentationToolbox.zip
which includes all the pre-compiled mex files in the right place meaning you can use the toolbox directly without having to compile the c++ source files by yourself.

Hope this can help.

[Yan Zhang]

Hi, Ning. One more thing: please don't use LCC compiler, it only supports C, NOT C++.

[Marco]

Hi Yan,

I tried to compile your toolbox on a linux system using gcc and still got some errors. I guess it would help linux people if you changed the following:

1. The comments in zy_binary_boundary_detection.c are not in ANSI C style. I know that double slashes are widely used, but in my case, I had to change all comments to be included in /* */ pairs. To make your code more widely compatible, changing this might help.
2. The error using std::exception is still there, because in BinaryHeap.c, line 56, you still pass an empty string to it. Replacing
 throw std::exception("");
by
 throw std::exception();
solved this for me.

After changing these two issues, everything compiled on my debian and R2008b.
Apart from that, thanks for sharing your code.

[Yan Zhang]

Hi Marco,

Thanks for your advices. For your Point 1, it's a strange problem, the file did pass my gcc 4.4 compiler on MacOSX. Then I tried to compile it on Ubuntu with the same compiler and it failed as you pointed out. As for Point 2, it's totally my fault.

[Cris Luengo]

This is a great starting point to explore active contours, thanks for the code!

On Marco's point 1: if you pass GCC the -std=c99 option it will allow the C++ style comments. They have only recently been added to the ANSI C standard. I agree that using /* */ comments is more portable.

[jichao zhao]

Could you provide your paper? I try to get your paper online, but it seems I can not. thanks

[Eran Ukwatta]

Hi Yan Zhang,
 Thanks for the code. By the way, I have a question. I am used to computing divergence of the level set function for the smoothness term. However in your code what I fould is linear diffusion. Are these two different things?
I also would like to add the edge based information to the chan-vese method for 3D segmentation. Is that straightforward as modifying the following evolving equation in the function "ac_ChanVese_model" ?

phi = phi + delta_t*image_weight*((I-mu_out).^2 - (I-mu_in).^2);

Thanks.

[Yan Zhang]

Hi Eran,

To answer your first question, let' s use u to represent the level-set, normally we use curvature flow to smooth the curve
u_t = div(\nabla u/|\nabla u|)
In my implementation, I do this in two steps:
(1) Make |\nabla u| = 1 using reinitialization (ac_reinit).
(2) With (1) the above equation can be simplified to
u_t = div(\nabla u) = \del u (the Laplacian of u)
which describes the linear diffusion of the level-set.
It's more efficient than solving the more general PDE
u_t = div(g \nabla u/|\nabla u|)
which leads to the answer to your second question --- you should look into the codes in "ac_GAC_model" (AOS implementation for geodesic active contour) that tells exactly how to integrate edge information.

[Jenny]

Hi,Zhang yan.Thank you for your toolbox.I have a problem.I'm trying to use your box to segment my own MRI head datas which are a series of JPEG or DICOM forms.Is your tool possible to segment this form of data.Or I must convert these formats to the supported formats.And how to?Thank you very much!

[Khin]

Hi Yan Zhang, When I read your 'test_ChanVese_model_3d.m' and 'test_hybrid_model_3d.m', I have a problem that cannot read head_ct.mat file. It's showing error "??? Error using ==> load Unable to read MAT file head_ct.mat. File may be corrupt." is it because of version different? I am using Matlab 6.5 please advise. thanks

[Alex Kararg]

Cannot compile running the compile_mex_codes.m . The output is :

expr: syntax error
/Applications/MATLAB_R2008a/bin/util/mex/mexutil.sh: line 13: [: too many arguments
ld warning: duplicate dylib /Applications/MATLAB_R2008a/bin/maci/libz.1.dylib
ld warning: duplicate dylib /Applications/MATLAB_R2008a/bin/maci/libz.1.dylib
ld warning: duplicate dylib /Applications/MATLAB_R2008a/bin/maci/libz.1.dylib
ld warning: duplicate dylib /Applications/MATLAB_R2008a/bin/maci/libz.1.dylib
ld warning: duplicate dylib /Applications/MATLAB_R2008a/bin/maci/libz.1.dylib
BinaryHeap.h: In member function 'void CBinaryHeapMinSort<IndexType, WeightType>::Insert(IndexType, WeightType) [with IndexType = int, WeightType = double]':
ac_distance_transform_3d.cpp:27: instantiated from 'void DistanceTransform3D(const InputType*, OutputType*, const int*) [with InputType = unsigned char, OutputType = double]'
ac_distance_transform_3d.cpp:115: instantiated from here
BinaryHeap.h:56: error: no matching function for call to 'std::exception::exception(const char [1])'
/usr/include/c++/4.0.0/exception:57: note: candidates are: std::exception::exception()
/usr/include/c++/4.0.0/exception:55: note: std::exception::exception(const std::exception&)

    mex: compile of ' "ac_distance_transform_3d.cpp"' failed.

??? Error using ==> mex at 207
Unable to complete successfully.

Error in ==> compile_mex_codes at 7
mex ac_distance_transform_3d.cpp

Any help to run the compile_mex_codes.m would be really appreciated. Thank you!

[Yan Zhang]

Hi Alex,

The problem has been fully discussed before, please see the previous comments for the details. In brief, go to the source file ac_distance_transform_3d.cpp, and get rid of the string in std::exception.

[Jenny]

hi ,Yan Zhang.Can I ask how did you get the results of Fig.5 in your paper "Medical Image Segmentation Using New Hybrid Level-Set Method",Did you use matlab or other tools to get the translucent head?

[Kai]

Hi Yan Zhang,
the GAC and the hybrid model does not work anymore. I changed my environment to windows 7 (64bit). When I run the examples in ac_GAC_model.m and ac_hybrid_model.m, I get the following error message: "MATLAB has encountered an internal problem and needs to close".
Everything works fine on Mac and 32bit Windows. The crash_dump says a "Segmentation violation detected" in ac_tridiagonal_Thomas_dll.mexw64.
Has anyone else this error?

[Yusuke Yoshiyasu]

Hi Yan Zhang,
Thanks for the toolbox. i have a question. If i want to apply your code to flux maximizing flow, where should i change? i think what i have to do is to change u_t = div(\nabla u) to u_t = div(\nabla I) or u_t = div(V), where I is some input image and V is vector field.
Thanks.

[Yan Zhang]

To Jenny,

The figure you mentioned was produced by a visualization software called Amira. As far as I know, the current matlab graphic toolbox doesn't support volume rendering.

[Yan Zhang]

To Yusuke,

The toolbox contains a AOS solver for the PDE in the form of u_t = div( g |\nabla u| ). This is a challenging problem because using explicit finite difference method (FDM) can cause unstability if the time step is too large.

For the PDE you mentioned, simple explicit FDM such as
u_(k+1) = u_k + delta_t * div(V)
should be working no matter how large delta_t is (of course the accuracy will be affected). The above scheme can be easily implemented in Matlab.

Hope this can help.

[adel khelifi]

Hi Yan Zhang,
i'm use Windows system,
when I used compile_mex_codes to compile, I met the following errors:

Error: Compile of 'ac_tridiagonal_Thomas_dll.cpp' failed.
 ??? Error using ==> mex at 221
Unable to complete successfully.
Error in ==> compile_mex_codes at 1
mex ac_tridiagonal_Thomas_dll.cpp
Error in ==> run at 57
          evalin('caller', [s ';']);
****************************************************************
i'm read this message
""a more complete version of the toolbox can be downloaded from the following link:
http://ecson.org/resources/software/_AOSLevelsetSegmentationToolbox.zip ""

please help me.

[Mark Brophy]

Hi Yan, thanks very much for the great software.

I am using your geodesic active contour model for 3d reconstruction. My problem is that I am having trouble updating the 'g' values on the surface. I have attempted to extract the surface using both Matlab's built-in isosurface and zy_binary_boundary_detection(uint8(phi>0)), but both of these commands only return a subset of the points on the surface. Basically, when I evolve the 3d surface, only a subset of the points 'move', so to speak.

Do you know how I might all points on the surface?

Cheers,
-Mark

[baoyun li]

Dr. Zhang:

Seems you renitilize level set at each step.
However, if not using narrow band, reintilization is very time consumming. Can I reinilized by narrowband and still use your AOS codes?

If use narrowband, how should I use AOS? I read the "fast geodesic levelset" paper, but don't understand how to apply AOS on Narrow band.

Thanks
Baoyun

[Amir]

good job!

[Stefan L.]

In fact a very useful tool.

I first used this toolbox in MATLAB R2008a and it worked pretty fine. Short time ago I switched to MATLAB R2009b (Windows 7, 64bit) and when using the tool I received one of the following errors:

Error type 1:

??? Error using ==> contourc
Input matrix contains no finite values - unable to calculate contours

Error in ==> contours at 57
CS=contourc(varargin{numarg_for_call});

Error in ==> ac_hybrid_model at 90
        c = contours(phi,[0,0]);

Error type 2:

MATLAB System Error
MATLAB has encountered an internal problem and needs to close.

Details:
MATLAB crash file:C:\Users\Stefan\AppData\Local\Temp\matlab_crash_dump.3776
------------------------------------------------------------------------
       Segmentation violation detected at Fri Apr 23 16:08:01 2010
------------------------------------------------------------------------
Configuration:
  MATLAB Version: 7.9.0.529 (R2009b)
  MATLAB License: 161051
  Operating System: Microsoft Windows Vista
  Window System: Version 6.1 (Build 7600)
  Processor ID: x86 Family 6 Model 7 Stepping 6, GenuineIntel
  Virtual Machine: Java 1.6.0_12-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode
  Default Encoding: windows-1252

Fault Count: 1

Stack Trace:
  [ 0] 000000007CEC59AB libmx.dll+022955 (mxCreateDoubleMatrix_730+000027)
  [ 1] 00000000369313A2 ac_tridiagonal_Thomas_dll.mexw64+005026 (mexFunction+000274)

At last I tracked down the problem in the MATLAB - bwdist() function which is used in the functions ac_reinit and ac_SDF_2D. In R2008a it returned an array of type double, in R2009b it returns an array of type single (despite the fact the documentation says it should be double).

After changing the line 25 in ac_reinit.m from
u = bwdist(u0).*sign(u); to u = double(bwdist(u0)).*sign(u);

and the lines 82, 91 and 120 in ac_SDF_2D.m from
phi = -bwdist(phi); to phi = -double(bwdist(phi));
phi = radius - bwdist(phi); to phi = radius - double(bwdist(phi));
phi = bwdist(phi); to phi = double(bwdist(phi));

everything worked fine again.

[Yan Zhang]

Hi, Stefan

Thanks a lot for sharing your invaluable experience! I guess this might be the reason why the toolbox fails to work on 64-bit operating system as reported before. I promise to correct this bug once I have access on 64-bit machine.

[Aureline]

Hello Yan, it seems you have done a great job here.

I cannot test your toolbox for now, I am using your pre-compiled version available on your website.
When I try to run one of the test files, I get the error
"Undefined function or method 'zy_binary_boundary_detection' for input arguments of type 'uint8'".
I have tried to get rid of the uint8 conversion in the ac_reinit file, but I still can't make the test run.
I am using 2010 version of Matlab, maybe the problem comes from here. Do you have any idea ?
Thanks a lot.

[Yan Zhang]

To Aureline,

Please type 'computer' in matlab and let me know what the result is. The precompiled version only works for 32bit windows system, yours may be 64bit.

[Yan Jianping]

Hello,Yan Zhang. when I used compile_mex_codes to compile, I met the following errors:

C:\DOCUME~1\yanjpphd\LOCALS~1\Temp\mex_933260AC-1398-46B6-6CA4-9F6BBF3212F4\ac_tridiagonal_Thomas_dll.obj
LINK : fatal error LNK1104: cannot open file "ac_tridiagonal_Thomas_dll.mexw32"
 
  C:\PROGRA~1\MATLAB\R2007B\BIN\MEX.PL: Error: Link of 'ac_tridiagonal_Thomas_dll.mexw32' failed.
 
??? Error using ==> mex at 208
Unable to complete successfully.

Error in ==> compile_mex_codes at 1
mex ac_tridiagonal_Thomas_dll.cpp

Thanks for your help!

[KSRaj Raj]

 

[Preeti]

Sir
 I am not able to compile the mex file. Got the following errors:
lcc preprocessor warning: C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp:95 No newline at end of file
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 7 syntax error; found `unsigned' expecting `;'
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 7 syntax error; found `unsigned' expecting `;'
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 7 syntax error; found `unsigned' expecting `)'
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 7 skipping `unsigned' `long' `int'
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 7 undeclared identifier `i'
Warning C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 7 Statement has no effect
Warning C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 7 unreachable code
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 7 syntax error; found `)' expecting `;'
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 7 illegal statement termination
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 7 skipping `)'
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 19 undeclared identifier `new'
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 19 operands of = have illegal types `pointer to double' and `int'
Warning C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 19 possible usage of new before definition
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 19 syntax error; found `double' expecting `;'
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 19 integer expression must be constant
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 19 missing identifier
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 51 undeclared identifier `delete'
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 51 illegal expression
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 51 syntax error; found `yy' expecting `]'
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 51 type error: pointer expected
Warning C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 51 Statement has no effect
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 51 syntax error; found `yy' expecting `;'
Warning C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 51 Statement has no effect
Warning C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 51 possible usage of delete before definition
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 71 illegal statement termination
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 71 skipping `double'
Error C:\PROGRA~1\MATLAB\R2008B\WORK\AOSLEV~1\MEX\ac_tridiagonal_Thomas_dll.cpp: 71 too many errors
 
  C:\PROGRA~1\MATLAB\R2008B\BIN\MEX.PL: Error: Compile of 'ac_tridiagonal_Thomas_dll.cpp' failed.
 
??? Error using ==> mex at 213
Unable to complete successfully.

Error in ==> compile_mex_codes at 1
mex ac_tridiagonal_Thomas_dll.cpp

Error in ==> run at 57
          evalin('caller', [s ';']);

please comment!

[emilie]

Hello,

I tried to compile the file "compile_mex_codes.m" but it it doesn't work correctly. It can not compile "zy_binary_boundary_detection.c". The following error appears:

??? Error using ==> mex at 208
Unable to complete successfully.

Error in ==> compile_mex_codes at 4
mex zy_binary_boundary_detection.c

Could you please help me. Thanks