[Insight-users] exclude pixel values (background) from metrics
Darren Weber
darren.weber.lists at gmail.com
Thu Mar 18 19:02:19 EDT 2010
Hi Luis et al.,
I'm puzzled by the intensityThreshold, because the optimizer observer gives:
Using fixed image intensity threshold: 1
0 nan [nan, nan, nan]
1 nan [nan, nan, nan]
2 nan [nan, nan, nan]
3 nan [nan, nan, nan]
4 nan [nan, nan, nan]
5 nan [nan, nan, nan]
6 nan [nan, nan, nan]
7 nan [nan, nan, nan]
8 nan [nan, nan, nan]
9 nan [nan, nan, nan]
10 nan [nan, nan, nan]
11 nan [nan, nan, nan]
12 nan [nan, nan, nan]
13 nan [nan, nan, nan]
14 nan [nan, nan, nan]
15 nan [nan, nan, nan]
16 nan [nan, nan, nan]
17 nan [nan, nan, nan]
18 nan [nan, nan, nan]
19 nan [nan, nan, nan]
20 nan [nan, nan, nan]
I'll try to explore a little more using the
BinaryThresholdImageFilter
I'll take a look at
examples/Filtering/BinaryThresholdImageFilter.cxx
Thanks,
Darren
On Wed, Mar 17, 2010 at 3:44 PM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
> Hi Darren,
>
> Excellent,
>
> In that case you should be able to eliminate the background
> by using:
>
> intensityThreshold = 1;
> metric->SetFixedImageSamplesIntensityThreshold( intensityThreshold );
>
> If you want to be 100% sure, it may be worth running a
> BinaryThresholdImageFilter first and saving the output
> for further visualization. That will provide a good sanity
> check.
>
>
> Regards,
>
>
> Luis
>
>
>
> ------------------------------------------------------------------------------------------
> On Wed, Mar 17, 2010 at 5:22 PM, Darren Weber
> <darren.weber.lists at gmail.com> wrote:
> >
> > 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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