[Insight-users] exclude pixel values (background) from metrics
Darren Weber
darren.weber.lists at gmail.com
Wed Mar 17 17:22:38 EDT 2010
Hi Luis et al.,
I've created the input images by exporting from Photoshop with a defined
background value (RGB: 0 0 0). It's these values that I want to exclude
from the metric in the image registration method.
The min color is confirmed by the identify program of ImageMagick:
Colorspace: RGB
Depth: 16-bit
Channel depth:
gray: 16-bit
Channel statistics:
Gray:
min: 0 (0)
max: 46335 (0.707027)
mean: 25664.6 (0.391617)
standard deviation: 15257.7 (0.232818)
kurtosis: -0.857968
skewness: -0.771191
TIA,
Darren
On Tue, Mar 16, 2010 at 10:25 AM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
> 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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