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Shape Context Based Corresponding Point Models

version 1.1 (18.5 MB) by

Shape Context based nonrigid registration of 2D/3D objects, to build Active Shape Models

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Shape Context is a method to get an unique descriptor (feature vector) for every point of an object contour or surface. This descriptor is used in combination with a b-spline free form deformation grid, for fully automatic creation of point mappings between surfaces of patient datasets (2D/3D).

The 2D Example will create a corresponding point model (PCM) for a set of 10 2D hand contours.

The 3D Example will create a PCM for a set of 10 3D jaw triangulated surfaces.

There are also examples using the PCM's to train and use 2D/3D Active Shape Models (ASM) and Active Appearance Models (AAM). (folder "ActiveModels_version7")

The 2D example takes a couple of minutes. The 3D-example about 7 hours, and requires 64bit Matlab.

The non-rigid mapping between datasets is kept Diffeomorphic to prevent mesh folding. But the optimizer doesn't succeeded in all cases of the 3D-example (maybe in next update)

Notes:
- The examples, will compile some c-coded functions into MEX files. In case of failure slower Matlab coded functions will be used.
- Most functions in this zip-archive are also available as standalone files on the File-Exchange, and can be newer/updated.

Comments and Ratings (21)

Xin Shu

Shingo Suzuki

Please, how i can create my manual landmark ?

nesrine

I have a CT-scan volume of liver and i want to generate the "land.mat" how i can get my "land.mat" fromy 3D data ? thank you a lot

For anyone looking to use these files, I've had to install a couple of toolboxes to get them working. Here is a list of the toolboxes I've installed.

Image Processing Toolbox
Statistics and Machine Learning Toolbox
System Identification Toolbox
Control System Toolbox
Signal Processing Toolbox

How can I get(define) the final measured by similarity (or sorted by similarity) value.

Hello. I performed image to image registration with your jaw data. But i would like to work with my own scapula data which i have as point cloud and not a volume, in stl or ply format. For the faces and vertices i can get these data and for the two different scales. But i don't have I1 volume available. Do you have a solution ? I'd like to try your algorithm because the scapula is a thin bone just like the jaw.

Thank you.

Silvia Wognum

When running the 2D example of ActiveModels_version7, I get an error message:

Undefined function or variable 'interp'.

Error in LoadDataSetNiceContour (line 21)
pointsx=interp(p.x,r); pointsx=pointsx(1:end-r+1);

Error in ASM_2D_example (line 60)
[Vertices,Lines]=LoadDataSetNiceContour(filename,options.ni,options.verbose);

Could it be that the function "interp" doesn't exist in Matlab 2015?

Instead, I tried to use the results of the asm example of creating the training set, but failed.

I hope you can help me solve this problem. I would like to use this example in my lecture on active shape models.

Silvia

Dirk-Jan Kroon

Dirk-Jan Kroon (view profile)

*Wong
Please, look for the references in:
http://www.k-zone.nl/Kroon_Thesis_small.pdf

WONG

WONG (view profile)

hello.can you tell me the original paper you referred to when writing the programs"Shape Context Based Corresponding Point Models".

Mark Sena

Trying to run on OSX 10.7.5, but getting the error:
/Applications/MATLAB_R2012a_Student.app/bin/mex: line 305: gcc-4.2: command not found
-> gcc-4.2 -c -I/Applications/MATLAB_R2012a_Student.app/extern/include -I/Applications/MATLAB_R2012a_Student.app/simulink/include -DMATLAB_MEX_FILE -fno-common -no-cpp-precomp -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -mmacosx-version-min=10.5 -fexceptions -DMX_COMPAT_32 -O2 -DNDEBUG "Features2CostMatrix.c"

/Applications/MATLAB_R2012a_Student.app/bin/mex: line 1326: gcc-4.2: command not found

mex: compile of ' "Features2CostMatrix.c"' failed.

Any help is appreciated.
Can't wait to use it!

Xiangqi

Xiangqi

Thank you for providing the code.

I am trying to use the ShapeContext function. It seems that the demo data "testdata.mat" in the folder "ShapeContext_version2" doesn't contain the correct data.

Dirk-Jan Kroon

Dirk-Jan Kroon (view profile)

*Birgit
Knnsearch is part of the "Statistics Toolbox" of Matlab. Maybe you can find a similar but free implementation on the File Exchange

Birgit

Birgit (view profile)

When I run BuildingModels\Example3D the function createns(), knnsearch() and maybe others called by Horn_Align_ICP are missing. Could the deliver be incomplete?

Birgit

Birgit (view profile)

Li Cheng

Li Cheng (view profile)

I found MATLAB code for active contours model in 1998 for a long time. Then found it. Really a good job!

l.l.

l.l. (view profile)

Hi! I don't understand how to set landmarks on my 3D dataset. I have to manually fix them on each image?
Thanks in advance and I apologize if the claim proves foolish.
L.

M M

M M (view profile)

how long should the 2D example take to run?

wang

wang (view profile)

why I can not download it?

Sebastien PARIS

A master piece ...

Updates

1.1

Many bugs solved. Less memory usage.

MATLAB Release
MATLAB 7.11 (R2010b)

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ActiveModels_version7/AAM Functions/

ActiveModels_version7/

ActiveModels_version7/ASM Functions/

ActiveModels_version7/Functions/

ActiveModels_version7/InterpFast_version1/

ActiveModels_version7/PatchNormals_version1/

ActiveModels_version7/PieceWiseLinearWarp_version2/

ActiveModels_version7/PieceWiseLinearWarp_version2/functions/

ActiveModels_version7/polygon2voxel_version1j/

BuildingModels/DistanceFieldCP_version1/

BuildingModels/DistanceFieldCP_version1/functions/

BuildingModels/DistanceFieldCP_version1/polygon2voxel_version1j/

BuildingModels/

BuildingModels/functions/

BuildingModels/isocontour_version2/

BuildingModels/nonrigid_version25/

BuildingModels/nonrigid_version25/functions/

BuildingModels/nonrigid_version25/functions_affine/

BuildingModels/nonrigid_version25/functions_nonrigid/

BuildingModels/nonrigid_version25/low_level_examples/

BuildingModels/polygon2voxel_version1j/

BuildingModels/ShapeContext_version2/

BuildingModels/ShapeContext_version2/functions/