[ITK] [ITK-users] Texture pixel by pixel

[Bradley Lowekamp]

Hello,

Use the source [1]! It's just a little debugging information, which should be changed to itkDebugMacro. Pull requests are welcomed.

The real offsets used relative to each pixel are the ones provided by "Offsets". What's printed out is all pairs used to generate the histogram in a neighborhood.

HTH,
Brad

[1] https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx#L129


On Sep 28, 2015, at 5:53 AM, Francisco Lopez de la Franca <franciscolopezdelafranca at gmail.com> wrote:

> Hi Bradley,
> I'm using your filter for a 3D image and the following is happpening: I store in a vector the offset list. When I print it, the list contains just 13 offsets (I've used the same code as in the itk::ScalarImageToTextureImageFilter). The problem comes when I call your SetOffsets(myOffsetList) method, my application starts printing a lot of offsets, I guess all the possible combinations for three dimensions.
> Do you know this "problem"? Then, what is the real offsets your filter use?
> 
> Thank you so much.
> Kind regards.
> /Francisco
> 
> 2015-09-25 15:10 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
> Hello,
> 
> For my itkTextureFeatureImageFilter, the default for the OffsetVector is an empty list. So it is required to set this member to get meaningful results.
> 
> ITK is an OpenSource project. When you don't know how something is implemented you can open the hood and find out [1].
> 
> HTH,
> Brad
> 
> [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Numerics/Statistics/include/itkScalarImageToTextureFeaturesFilter.hxx#L66-L76
> 
> On Sep 25, 2015, at 6:37 AM, Francisco Lopez de la Franca <franciscolopezdelafranca at gmail.com> wrote:
> 
>> Which directions (for 3D images) will your filter use if I donot specify any offset?
>> 
>> 2015-09-25 11:12 GMT+02:00 Francisco Lopez de la Franca <franciscolopezdelafranca at gmail.com>:
>> Hi again,
>> 
>> For 3D images, what should I use as default offset vector if I use your class?
>> 
>> I've been using itk::ScalarImageToTextureFeaturesFilter for 3D images and I've also done some tests on 3D NIFTI images but its description talks only about the default 2D image offsets ({(-1, 0), (-1, -1), (0, -1), (1, -1)}) but not for 3D. Besides, the 2D default is missing some offsets.
>> 
>> I'd like to use your class and test it with the same default values as with the ScalarIm.... class.
>> 
>> Thank you very much.
>> My best regards.
>> 
>> 
>> 2015-09-22 14:27 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>> Hello,
>> 
>> Please try to keep this discussion on the mailing list.
>> 
>> You can find a basic program here [1].  Which provide a good example for usage.
>> 
>>  It allows writing to any file format that ITK supports with vector images. I know that mha, nii, and nrrd should support this. Others may and it varies based what modules are compiled into ITK.
>> 
>> You can see how the texture information is written into the vector here [2]. Contributions to improve the documentation are welcomed.
>> 
>> 
>> 
>> [1] https://github.com/blowekamp/itkTextureAnalysis/blob/master/test/itkTextureFeatureImageFilterTest.cxx
>> [2] https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx#L217-L224
>> 
>> On Sep 22, 2015, at 3:25 AM, Francisco Lopez de la Franca <franciscolopezdelafranca at gmail.com> wrote:
>> 
>>> Hi Bradley,
>>> I'd like to use your class. A couple of questions:
>>> 
>>> - Which format can the vectorimage generated be saved in? Is it possible to save it in Nifti format?
>>> 
>>> - Which information does the vector image contain, I mean, what is the info stored for each voxel? How can I access that info?
>>> 
>>> I guess the usage of yourclass is in the same way as any ITK filter:
>>> 
>>> yourFilter->setInput(inputImage);
>>> yourFilter->setWindowSize(windowSize);
>>> ... // other sets...
>>> yourFilter->update();
>>> vectorImage = yourFilter->GetOutput();
>>> 
>>> but, how can I read the data of each voxel in the vector image?
>>> 
>>> Thank you very much.
>>> Kind regards.
>>> 
>>> 
>>> 2015-09-21 14:30 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>>> Hello,
>>> 
>>> I have a external ITK extension you may find useful:
>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h
>>> 
>>> This computed the GLCM, for a neighborhood for every pixel and produces a VectorImage with all the features.
>>> 
>>> Contributions to improving the class and documentation are welcome.
>>> 
>>> HTH,
>>> Brad
>>> 
>>> On Sep 21, 2015, at 7:15 AM, Francisco Lopez de la Franca <franciscolopezdelafranca at gmail.com> wrote:
>>> 
>>> > Hi,
>>> > I've used the itk::Statistics::ScalarImageToTextureFeaturesFilter class with the default parameters and everything was OK.
>>> >
>>> > But now, I have to calculate the texture features of a 2D scalar image pixel by pixel, I mean, iterate over the whole image and calculate the texture features of every pixel.
>>> >
>>> > I guess I've got to use each pixel as the masked region over which to calculate the texture features, but I think this process could be very slow (I have to do it with a lot of 2D images).
>>> >
>>> > Is there a faster way to do it or isn't it possible as I've described?
>>> >
>>> > Thanks a lot.
>>> > Kind regards.
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>>> 
>> 
>> 
>> 
> 
> 

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