[ITK] [ITK-users] Texture analysis - two basics questions
Dženan Zukić
dzenanz at gmail.com
Wed Jan 13 11:08:20 EST 2016
Hi Yohann,
line 56 in your TextureFeature.cxx:
glcmGenerator->SetPixelValueMinMax(0, 255); //for input UCHAR pixel type
could be the culprit. The input files in my example
<http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures> were uchar,
and 0-255 range was OK. For general processing, you should use minMax finder
<http://www.itk.org/Doxygen/html/classitk_1_1MinimumMaximumImageCalculator.html>
and
pass those 2 values to calcTextureFeatureImage function. Your
*Example_DataMatrix.csv* contained values over 255 (300+), but not a lot of
them. The other image might have higher maximum values or negative minimum
values, which would cause more anomalies such as NaNs.
As for conversion of DICOM to MHA or NRRD, you can use Slicer for that.
Just import it via DICOM module, and then save them with .mha or .nrrd
extension. Then you can read them easily via itk::ImageFileReader.
HTH,
Dženan
On Tue, Jan 12, 2016 at 6:18 PM, Yohann Tschudi <yxt227 at med.miami.edu>
wrote:
> Ok, I finally implemented everything and I got a "result".
> It means I got an 3D image (.mha) for each features with some numbers
> different from nan (I do not understand yet how that is possible).
> Here is an example of outputs for this study:
> _Energy0.mha
> <http://itk-insight-users.2283740.n2.nabble.com/file/n7588348/_Energy0.mha
> >
> _Correlation0.mha
> <
> http://itk-insight-users.2283740.n2.nabble.com/file/n7588348/_Correlation0.mha
> >
>
> However for another study, I got 0 or nan or out of frame (I am using
> 3Dslicer to vizualise .mha, it gives me directly the value for each pixel
> pointed by the mouse).
> Example2_Energy0.mha
> <
> http://itk-insight-users.2283740.n2.nabble.com/file/n7588348/Example2_Energy0.mha
> >
> Example2_Correlation0.mha
> <
> http://itk-insight-users.2283740.n2.nabble.com/file/n7588348/Example2_Correlation0.mha
> >
>
> I am a bit confused but I think this is coming from the construction of the
> input/3d data matrix.
>
> Let me explain what I am trying to do:
> I have an input file containing all the information of the data (a cube
> containing a prostate volume with T2 values (0 outside the prostate)):
> -> the first line contains the size of the matrix width, height and depth
> -> for each line, the value for each pixel
> Example:
> Example_DataMatrix.csv
> <
> http://itk-insight-users.2283740.n2.nabble.com/file/n7588348/Example_DataMatrix.csv
> >
> 74 60 17
> 0 0 0 0.0
> 0 0 1 0.0
> 0 0 2 0.0
> ...
> 11 42 3 0.0
> 11 42 4 290.0
> 11 42 5 265.0
> 11 42 6 269.0
> ...
> 73 59 14 0.0
> 73 59 15 0.0
> 73 59 16 0.0
>
> This data matrix is then transformed in itk::Image<float, 3>
> InternalImageType image (I think there is a problem here maybe):
> /int Create3DImageFromMatrix(InternalImageType::Pointer &_image, string
> _dataMatrixFile)
> {
> //Create image
> InternalImageType::Pointer image = InternalImageType::New();
>
> // Get file
> std::cout << "Get data matrix file " << _dataMatrixFile << endl;
> ifstream dataFile(_dataMatrixFile);
>
> //Read file
> string line;
> int xSize = 0;
> int ySize = 0;
> int zSize = 0;
> int iLine = 0;
> while (getline(dataFile, line))
> {
> istringstream iss(line);
> if (iLine == 0)
> {
> //First line size of matrix
> iss >> xSize >> ySize >> zSize;
> std::cout << "Data matrix size verification: " <<
> xSize << "x" << ySize
> << "x" << zSize << endl;
>
> //Initialize image
> InternalImageType::RegionType region;
> InternalImageType::IndexType start;
> start[0] = 0;
> start[1] = 0;
> start[2] = 0;
> InternalImageType::SizeType size;
> size[0] = xSize;
> size[1] = ySize;
> size[2] = zSize;
> region.SetSize(size);
> region.SetIndex(start);
> image->SetRegions(region);
> image->Allocate();
>
> ++iLine;
> }
> else
> {
> //Fill image
> int x, y, z;
> double value;
> if (!(iss >> x >> y >> z >> value))
> {
> return -1;
> }
> else
> {
> InternalImageType::IndexType pixelIndex;
> pixelIndex[0] = x;
> pixelIndex[1] = y;
> pixelIndex[2] = z;
> image->SetPixel(pixelIndex, value);
> ++iLine;
> }
> }
> }
>
> _image = image;
> std::cout << "Image created from data matrix file" << endl;
> return 0;
> }/
>
> Finally, the code to compute the features is the same (in 3D) than in the
> example :
> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures
> <http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures>
> / int index0 = inputImage->GetLargestPossibleRegion().GetSize(0);
> int index1 = inputImage->GetLargestPossibleRegion().GetSize(1);
> int index2 = inputImage->GetLargestPossibleRegion().GetSize(2);
>
> //slide window over the entire image
> for (unsigned x = 1; x < index0 - 1; x++)
> {
> pi.SetElement(0, x);
> window.SetIndex(0, x - 1);
> for (unsigned y = 1; y < index1 - 1; y++)
> {
> pi.SetElement(1, y);
> window.SetIndex(1, y - 1);
> for (unsigned z = 1; z < index2 - 1; z++)
> {
> pi.SetElement(2, z);
> window.SetIndex(2, z - 1);
> roi->SetRegionOfInterest(window);
> roi->Update();
> glcmGenerator->SetInput(roi->GetOutput());
> glcmGenerator->Update();
>
> featureCalc->SetInput(glcmGenerator->GetOutput());
> featureCalc->Update();
>
>
> outInertia->SetPixel(pi,featureCalc->GetFeature(Hist2FeaturesType::Inertia));
> outCorrelation->SetPixel(pi,
> featureCalc->GetFeature(Hist2FeaturesType::Correlation));
> outEnergy->SetPixel(pi,
> featureCalc->GetFeature(Hist2FeaturesType::Energy));
> outEntropy->SetPixel(pi,
> featureCalc->GetFeature(Hist2FeaturesType::Entropy));
> }
> }
>
> //Print step
> int total = index0 - 2;
> string step = to_string(x) + " on " + to_string(total);
> std::cout << step << endl;
> }/
>
> As I wrote upper, the output values for this last example are either 0 or
> nan or out of frame.
> I am pretty sure that for the first example, getting values different from
> 0 are lucky (I still have nan values in it though).
> I am missing something and I am looking since hours without seeing what is
> wrong. Hope this is obvious ...
>
> Here is the c++ file I am using :
> TextureFeatures.cxx
> <
> http://itk-insight-users.2283740.n2.nabble.com/file/n7588348/TextureFeatures.cxx
> >
>
> Thank you for your help
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588348.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
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