[Insight-users] SpatialObjectToImageFilter run time

[Cagatay Bilgin]

Hi Dan,

thank you for the prompt response. I do have both v3(3.20) and v4 and
unfortunately the code does not compile on v3 either. The problem is not v3
vs v4, but missing variables and typedefs in the class definition

Here are the first few lines from the compilation process

In file included from tkMaskedSpatialObjectToImageFilter.cxx:20:0:
itkMaskedSpatialObjectToImageFilter.h:73:37: error: ‘OutputImageDimension’
was not declared in this scope
itkMaskedSpatialObjectToImageFilter.h:73:57: error: template argument 2 is
invalid
itkMaskedSpatialObjectToImageFilter.h:74:20: error: ‘MaskImageType’ is not
a class or namespace
itkMaskedSpatialObjectToImageFilter.h:75:20: error: ‘MaskImageType’ is not
a class or namespace
itkMaskedSpatialObjectToImageFilter.cxx: In constructor
‘itk::MaskedSpatialObjectToImageFilter<TInputSpatialObject,
TOutputImage>::MaskedSpatialObjectToImageFilter()’:
itkMaskedSpatialObjectToImageFilter.cxx:43:3: error: ‘m_ChildrenDepth’ was
not declared in this scope
itkMaskedSpatialObjectToImageFilter.cxx:44:3: error: ‘m_Size’ was not
declared in this scope
itkMaskedSpatialObjectToImageFilter.cxx:46:32: error:
‘OutputImageDimension’ was not declared in this scope
itkMaskedSpatialObjectToImageFilter.cxx:48:5: error: ‘m_Spacing’ was not
declared in this scope
itkMaskedSpatialObjectToImageFilter.cxx:49:5: error: ‘m_Origin’ was not
declared in this scope
itkMaskedSpatialObjectToImageFilter.cxx:52:3: error: ‘m_InsideValue’ was
not declared in this scope
itkMaskedSpatialObjectToImageFilter.cxx:53:3: error: ‘m_OutsideValue’ was
not declared in this scope
itkMaskedSpatialObjectToImageFilter.cxx:54:3: error: ‘m_UseObjectValue’ was
not declared in this scope
itkMaskedSpatialObjectToImageFilter.cxx: In member function ‘virtual void
itk::MaskedSpatialObjectToImageFilter<TInputSpatialObject,
TOutputImage>::SetupOutputImage()’:

Cagatay

On Tue, Feb 5, 2013 at 8:40 PM, Dan Mueller <dan.muel at gmail.com> wrote:

> Hi Cemal,
>
> The problem is in the design of the SpatialObjectToImageFilter. This
> filter iterates over the entire image and for each pixel queries
> whether the spatial object resides in the current pixel. The
> MaskedSpatialObjectToImageFilter attempts to alleviate this issue by
> only querying the spatial object for pixels which are likely to
> contain the object. This approach only works for sparse spatial
> objects i.e. objects which do not fill the entire image. The
> MaskedSpatialObjectToImageFilter  Insight Journal submission was
> written for ITKv3 and is evidently now broken for ITKv4. Unfortunately
> I don't have time to help getting it compile with ITKv4.
>
> Another approach is improve speed is to iterate only the bounding box
> of each object. I implemented this approach (though not for
> SpatialObjects) here:
>
> http://code.google.com/p/manageditk/source/browse/trunk/Source/Modules/IntensityFilters/itkGenerateMaskImageFilter.h
>
> http://code.google.com/p/manageditk/source/browse/trunk/Source/Modules/IntensityFilters/itkGenerateMaskImageFilter.txx
> This filter allows you to specify a number of ellipses, boxes, and
> points to generate a mask image. Again, this code was written for
> ITKv3 and may not compile with ITKv4...
>
> Good luck.
>
> Regards, Dan
>
> On 6 February 2013 12:50, Cagatay Bilgin <bilgincc at gmail.com> wrote:
> > Hi, I've been using SpatialObjectToImageFilter for a while to create
> > synthetic images and have been upset with the run time. For 10 ellipse
> > objects (3d) the run time is 1 minute, for 20 objects it's around 5
> minutes.
> > Everything is compiled in release mode, and the rest of the kit runs as
> > expected.
> >
> > I found an email on the emailing list where Dan Mueller suggests using
> > MaskedSpatialObjectToImageFilter
> >
> http://itk-users.7.n7.nabble.com/SpatialObjectToImageFilter-slow-td27261.html
> > Unfortunately the code does not compile; some typedefs are not defined,
> and
> > some variables are not declared. I tried fixing them and got it to
> compile
> > but when I tried running the example I got a blank image. Do you have any
> > suggestions?
> >
> > Thanks,
> > Cagatay
> >
> >
> > --
> > Cemal Cagatay Bilgin
> > Life Sciences Division
> > Lawrence Berkeley National Lab
> > MS977, One Cyclotron Road
> > Berkeley, CA 94720, USA
> > Email: ccbilgin at lbl.gov
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>



-- 
Cemal Cagatay Bilgin
Life Sciences Division
Lawrence Berkeley National Lab
MS977, One Cyclotron Road
Berkeley, CA 94720, USA
Email: ccbilgin at lbl.gov <hchang at lbl.gov>
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