[Insight-users] exclude pixel values (background) from metrics
Luis Ibanez
luis.ibanez at kitware.com
Tue Mar 16 13:25:06 EDT 2010
Hi Darren,
1) As described in the ITK Software Guide
http://www.itk.org/ItkSoftwareGuide.pdf
in the Chapter 7 "Reading and Writing Images",
in section 7.1, pdf-page: 296:
ITK takes the pixel data from the input file and casts it to
the PixelType that you used for instantiating your image
at compilation time. The casting is performed using
C-Language rules, and not truncation, overflow or underflow
detection, nor scaling is applied.
So, if your TIFF file contains 16bit integers values per pixel
and you instantiate the image using a "float" pixel type, then
the values of the integers will be casted (without any rescaling)
in to floats.
2) If you have a use for the original "16bits" data, then it may
be worth reading the file in an image of the exact same type
and then using a CastImageFilter to convert it to float.
On the other hand, if you only need the float image for
performing the registration, then reading directly into a
float image is actually saving you some memory.
3) "Black" pixels is quite an ambiguous measure, since,
depending on the image viewer that you are using, it may
well be that what you "see" as black, is actually a level
of intensity with values around 20,000 (for example).
What you really need is a sort of histogram that will allow
you to identify the background of the image,
or
A visualization method that allows you to identify the
intensity level of the background.
You may want to consider:
Insight/Code/Algorithms/
itkOtsuThresholdImageCalculator.h
and the Insight Journal papers:
"Kappa Sigma Clipping"
http://www.insight-journal.org/browse/publication/132
http://hdl.handle.net/1926/367
"Robust Automatic Threshold Selection"
http://www.insight-journal.org/browse/publication/134
http://hdl.handle.net/1926/370
as options for estimating a suitable threshold.
Regards,
Luis
----------------------------------------------------------------
On Mon, Mar 15, 2010 at 3:09 PM, Darren Weber
<darren.weber.lists at gmail.com> wrote:
>
> Hi Luis et al.,
>
> Now the ITK library is compiled and installed with the additional features
> available. Now this code will compile:
>
> typedef itk::MeanSquaresImageToImageMetric<iBWImgType,iBWImgType>
> MetricType;
> MetricType::Pointer metric = MetricType::New();
> metric->SetUseFixedImageSamplesIntensityThreshold( true );
> metric->SetFixedImageSamplesIntensityThreshold( intensityThreshold );
> //metric->SetUseSequentialSampling( true );
> //metric->SetUseAllPixels( true );
>
>
> Now a question arises about the range of values for the
> "intensityThreshold". The input pixel and image typedefs are:
>
> const unsigned short dimImg = 2;
> typedef float iPixType;
> typedef itk::Image< iPixType, dimImg > iBWImgType;
> typedef itk::ImageFileReader< iBWImgType > bwImageReaderType;
>
>
> The image reader is pulling in .tif images, which ImageMagick identifies as
> (see verbose output in attachment):
>
> $ identify testdata/bw/section0003_w1.tif
> testdata/bw/section0003_w1.tif TIFF 549x539 549x539+0+0 16-bit Grayscale
> DirectClass 615KB 0.010u 0:00.030
>
> When this image is read into the iPixType, I assume the range of these
> "unsigned short" values is mapped or cast into a range of "float" values.
> Is the new range of values from 0.0 to 1.0, is that correct for the "float"
> pixel type in ITK? How does the ITK image reader convert or cast the pixel
> values to float? (The reason the input images are specified as "float"
> rather than "unsigned short" is to have them input to the registration
> method as floats - should this be done with an explicit cast filter?)
>
> The input images have a black background (RGB value: 0 0 0). It would be
> great to threshold the MeanSquaresImageToImageMetric to exclude all the
> black pixels. In the range of values for the input pixel data that are an
> unsigned short (0 to 65535), any pixel above 0 would be
>
> unsigned short intensityThreshold = 1;
>
> However, the intensityThreshold is declared and initialized as:
>
> iBWImgType::PixelType intensityThreshold = 0.0;
>
> Is this a reasonable value for this float intensityThreshold:
>
> iBWImgType::PixelType intensityThreshold = 1.0 / USHRT_MAX;
>
>
> TIA,
> Darren
>
>
>
>
> On Sat, Mar 6, 2010 at 12:15 PM, Luis Ibanez <luis.ibanez at kitware.com>
> wrote:
>>
>> Hi Darren,
>>
>> The feature that you are referring to, is only available
>> in the new version of the metrics that are in the
>> Code/Review directory.
>>
>> In order to use this classes you must reconfigure your
>> binary build of ITK, by rerunning CMake and turning
>> ON the CMake variables:
>>
>> * ITK_USE_REVIEW
>> * OPTIMIZED_REGISTRATION_METHODS
>>
>> Then you can rebuild your application.
>>
>>
>> Regards,
>>
>>
>> Luis
>>
>>
>>
>> -----------------------------------------------------------------------------------
>> On Thu, Mar 4, 2010 at 5:56 PM, Darren Weber
>> <darren.weber.lists at gmail.com> wrote:
>> >
>> > In an image registration framework, the metric determines image
>> > "matches".
>> > Let's suppose we have large images that contain a majority of background
>> > color (or transparency). In a metric like the
>> > itk::MeanSquaresImageToImageMetric, the majority of the
>> > sqaured-diff-values
>> > would be zero and the remainder of the "relevant" pixel differences may
>> > be
>> > "swamped" or "lost" in the division by a large N.
>> > Also, it appears the default metric sampling is a random-sample of the
>> > image
>> > pixels (this might be modified with methods like
>> > "SetUseAllPixels(bool)").
>> > In this case, it is possible, perhaps likely, that few of the
>> > "relevant"
>> > pixels will be evaluated in the metric.
>> > See:
>> >
>> > http://www.itk.org/Doxygen316/html/classitk_1_1ImageToImageMetric.html#42b876134388099afbf34b14faf83cdb
>> > This documentation suggests there are also options to define:
>> > IntensityThreshold, Masks, and SequentialSampling
>> > In my reading of the doxy page (see next link), there is a method called
>> > "SetFixedImageSamplesIntensityThreshold" that might be useful to define
>> > a
>> > background value (like zero) to be excluded from the metric. Is that
>> > right?
>> >
>> > http://www.itk.org/Doxygen316/html/classitk_1_1MeanSquaresImageToImageMetric-members.html
>> > What is the logic of this "threshold" method? From the documentation,
>> > it
>> > appears to be a minima value. So if the background intensity is zero,
>> > the
>> > threshold value of 1 would include all pixels > 0 (note the threshold
>> > value
>> > must be the same type as the fixed image PixelType).
>> > There is no equivalent method for the moving image,
>> > like "SetMovingImageSamplesIntensityThreshold". Is this unnecessary
>> > because
>> > the metric only scans the pixels of the moving image that fall within
>> > the
>> > "domain" of fixed image after the transform & interpolation?
>> > I could not locate this method in the class hierarchy - is it available
>> > (inherited) in all metrics?
>> > I'm confused because these methods do not appear to be available
>> > to itk::MeanSquaresImageToImageMetric
>> > e.g.: CODE:
>> > typedef itk::MeanSquaresImageToImageMetric< iBWImgType, iBWImgType >
>> > MetricType;
>> > MetricType::Pointer metric = MetricType::New();
>> > metric->SetFixedImageSamplesIntensityThreshold( 0.0 );
>> > metric->SetUseAllPixels( true );
>> > e.g.: COMPILATION:
>> > itkImageRigid2DCoregistration.cxx: In function ‘int main(int, char**)’:
>> > itkImageRigid2DCoregistration.cxx:442: error: ‘class
>> > itk::MeanSquaresImageToImageMetric<iBWImgType, iBWImgType>’ has no
>> > member
>> > named ‘SetFixedImageSamplesIntensityThreshold’
>> > itkImageRigid2DCoregistration.cxx:443: error: ‘class
>> > itk::MeanSquaresImageToImageMetric<iBWImgType, iBWImgType>’ has no
>> > member
>> > named ‘SetUseAllPixels’
>> > gmake[2]: ***
>> >
>> > [CMakeFiles/itkImageRigid2DCoregistration.dir/itkImageRigid2DCoregistration.cxx.o]
>> > Error 1
>> >
>> >
>> >
>> > TIA,
>> > Darren
>> >
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