[ITK-users] Texture pixel by pixel

Mon Sep 28 05:53:56 EDT 2015

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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