Fw: [Insight-users] How to compute "PCA s hape model"?
sun
kacking123 at 163.com
Wed May 31 08:29:45 EDT 2006
Hi Zach:
The program can finish now ,but the result is error. there are nothing in the output image.
here are the outputs of this program. Whether there are something else i needed to do ?
E:\ITK\bin>g3 n46.tif s1.tif 135 337 156 354 180 371 1 1 0.5 0.02 m1.mha 3 pca 1
35 330
1: 0.217925 [0, 0, 0, 0, 135, 330]
2: 0.217924 [0, 0, 0, 0, 135, 330]
3: 0.219151 [0, 0, 0, 0, 135, 330]
4: 0.219156 [0, 0, 0, 0, 135, 330]
5: 0.219156 [0, 0, 0, 0, 135, 330]
6: 0.219156 [0, 0, 0, 0, 135, 330]
7: 0.219156 [0, 0, 0, 0, 135, 330]
8: 0.249912 [0, 0, 0, 0, 135, 330]
9: 0 [0, 0, 0, 0, 135, 330]
Max. no. iterations: 400
Max. RMS error: 0.005
No. elpased iterations: 9
RMS change: 0
Parameters: [0, 0, 0, 0, 135, 330]
Thanks
sunli
----- Original Message -----
From: sun
To: zpincus at stanford.edu ; insight-users at itk.org
Sent: Wednesday, May 31, 2006 2:58 PM
Subject: Fw: [Insight-users] How to compute "PCA s hape model"?
Hi Zach:
I have find some test code of itkImagePCAShapeModelEstimator class, and generated mean image and 3 PCAShapeModel outputs successfully(all in mha files).
But when i gave them to the quoted code of Geodesic Active Contours Segmentation with Shape Guidance, an error occured and the program aborted. I want to know whether there are something else i needed to do ?
Thanks
sunli
----- Original Message -----
From: sun
To: insight-users ; zpincus at stanford.edu
Sent: Tuesday, May 30, 2006 7:49 PM
Subject: Re: [Insight-users] How to compute "PCA s hape model"?
Hi Zach :
I have generated three Signed Distance Maps with SignedDanielssonDistanceMapImageFilter,and stored them in mha files,I want to use them as the TrainingImage. Now i have a question that how can i give these inputs to the itkImagePCAShapeModelEstimator? There are 3 TrainingImages and they are accessed using "this->getinput(0),this->getinput(1),this->getinput(2) in the itkImagePCAShapeModelEstimator class.
Here is my code, it can't work.
const unsigned int Dimension = 2;
typedef float my_PixelType;
typedef itk::Image< my_PixelType, Dimension > signdis_ImageType;
std::vector<signdis_ImageType::Pointer> signdisImages( 3 );
typedef itk::ImageFileReader< signdis_ImageType > ReaderType;
typedef itk::ImageFileWriter< signdis_ImageType > WriterType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
reader->SetFileName( argv[1] );
reader->Update();
signdisImages[0] = reader->GetOutput();
reader->SetFileName( argv[2] );
reader->Update();
signdisImages[1] = reader->GetOutput();
reader->SetFileName( argv[3] );
reader->Update();
signdisImages[2] = reader->GetOutput();
typedef itk::ImagePCAShapeModelEstimator<
signdis_ImageType,
signdis_ImageType > my_Estimatortype;
my_Estimatortype::Pointer filter = my_Estimatortype::New();
filter->SetInput( signdisImages ); // error here!!!!!!!!!!!!!!!!!!!!!
writer->SetFileName( argv[4] );
writer->SetInput( filter->GetOutput(0) );
writer->Update();
writer->SetFileName( argv[5] );
writer->SetInput( filter->GetOutput(1) );
writer->Update();
........
Thanks
sunli
----- Original Message -----
From: "Zachary Pincus" <zpincus at stanford.edu>
To: "sun" <kacking123 at 163.com>
Cc: <insight-users at itk.org>
Sent: Tuesday, May 30, 2006 2:55 AM
Subject: Re: [Insight-users] How to compute "PCA shape model"?
> Hi Zach :
> Thank you for your reply.
> I have read the code in itkImagePCAShapeModelEstimator.txx . It
> seems that the mean image and principal component outputs are
> generated in this class,and the inputs of this class is
> TrainingImages.
This is correct.
> So i wondered what the "signed distance maps a set of
> training shapes " mean in your reply, and how can i input these
> images.
Use one of the Signed Distance Map filters available in ITK (there
are several, check out the Doxygen class list) to convert binary
training images (spanning the space of possible shapes you wish to
segment) into signed distance maps, where each pixel's value is the
distance from that pixel to the nearest edge of the binary object
(and the pixel's value is negative if it is inside the object). This
then represents each shape as the zero-level set of an image.
> In the quoted code, the shape model defined by
> CorpusCallosumMeanShape.mha and the first three principal
> components CorpusCallosumMode0.mha, CorpusCallosumMode1.mha and
> CorpusCallosumMode12.mha. How can i generate
> these mha files? Can i write the principal component outputs of
> itkImagePCAShapeModelEstimator class in mha files
> directly?
That is correct. Or you could use them directly without writing them
to files.
>
> Thanks
> Sunli
>
> ----- Original Message -----
> From: "Zachary Pincus" <zpincus at stanford.edu>
> To: "sun" <kacking123 at 163.com>
> Cc: "itk" <insight-users at itk.org>
> Sent: Sunday, May 28, 2006 3:41 AM
> Subject: Re: [Insight-users] How to compute "PCA shape model"?
>
>
>
> This is a longstanding gap in the documentation.
>
> In brief, you will need to generate signed distance maps of a set of
> training shapes, and pass them to the PCAShapeModelEstimator class.
> You may then choose to divide the returned "shape mode" images (note
> that output zero from the model estimator is the mean image) by the
> reported standard deviations, as described in the example.
>
> Let me know if more detail is required.
>
> Zach Pincus
>
> Program in Biomedical Informatics and Department of Biochemistry
> Stanford University School of Medicine
>
>
> On May 27, 2006, at 12:06 AM, sun wrote:
>
>> Hi all:
>> I am using the filter "Geodesic Active Contours Segmentation
>> with Shape Guidance" to
>> segment my image now.But the quoted code just reads in a "PCA
>> shape model" that has been pre-computed
>> earlier. I want to know how to compute such a shape model in ITK.
>> Who can help me?
>> sun li
>>
>>
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