[Insight-users] Masking a region & thresholding
Luis Ibanez
luis.ibanez at kitware.com
Mon, 09 Feb 2004 22:28:29 -0500
Hi Radhika,
You certainly don't want to use iterators
for altering directly an image in the
middle of the pipeline. All your changes
will be lost the next time you update the
filters.
You should probably look at the AND, OR
filter and actually mask the gray levels
of the input image using your mask. Then
continue the pipeline with an image that
has the original gray level on the region
of the mask and zeros elsewhere.
http://www.itk.org/Insight/Doxygen/html/classitk_1_1OrImageFilter.html
http://www.itk.org/Insight/Doxygen/html/classitk_1_1AndImageFilter.html
Regards,
Luis
-------------------------------
Radhika Sivaramakrishna wrote:
> Hi Luis,
>
> Thanks for entering this as a bug.
> You are right about the cumulators. I should declare them as float.
> I do not understand the issue you pointed to below.
>
> I am forced to do my calculations this way because what I want to do is
> the following:
>
> Use the histogram analysis to identify a threshold to threshold the
> image. But I want to do the thresholding only in the region of the mask.
> Ie I am basically happy my mask, except it also includes regions in the
> original image that are higher than the threshold which I want to remove.
>
> If
> I just use this threshold through a standard Threshold filter, then I
> will end up with a lot of other regions (values lower than this
> threshold that I don't need), so I am constraining this thresholding
> only in the region of the mask, so I am directly editing the ON pixels
> in my mask to switch off at regions in the gray level that are higher
> than threshold. Is there a better way to do this?
>
> Radhika
>
>
> -----Original Message-----
> From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
> Sent: Monday, February 09, 2004 11:59 AM
> To: Radhika Sivaramakrishna
> Cc: ITK; Miller, James V (Research)
> Subject: Re: [Insight-users] Compilation error with inPlace filters
>
>
> Hi Radhika,
>
> This seems to be a bug in the RelabelImageFilter.
> The issue has been entered in the bug tracker with ID # 582
>
> http://www.itk.org/Bug/bug.php?op=show&bugid=582&pos=0
> <http://www.itk.org/Bug/bug.php?op=show&bugid=582&pos=0>
>
> In the meantime, please instantiate the RelabelImageFilter
> using the same image type for input and output.
>
> ----
>
> Unrelated to the error above,... but still worrisome:
>
> In your code you are taking the output of a reader and
> using an iterator for changing the value of this image.
> (the "mask" image in lines 193 - 201 ).
>
> Then you pass the image as input to another filter.
> This is a violation of the pipeline encapsulation.
> You should use a threshold image filter instead of
> using an iterator through the image. The output of the
> filters should be const... but we still have this
> weakness in ITK filters....
>
> The cumulators that you have for frequencies are
> being declared unsigned long. They should be floats
> or doubles. Note that Frequencies are not just counters,
> they actually provide floating point values.
>
>
> Regards,
>
>
> Luis
>
>
> ---------------------------------------
> Radhika Sivaramakrishna wrote:
>
> > Hi Luis,
> > I actually did the checkout this morning and I did see the Dashboard
> > was pretty green. I don't know if I am making a silly mistake or a
> > more serious error.
> >
> > I have copied my code here which doesn't compile and gives the error
> > indicated below. I think the problem has something to do with the
> > IntImageType I put in for dealing with the Relabel.. filter.
> >
> > Sorry about not putting the correct subject. Will try to make sure to
> > do it from now on.
> >
> > Radhika
> >
> >
> > -----Original Message-----
> > From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
> > Sent: Monday, February 09, 2004 10:34 AM
> > To: Radhika Sivaramakrishna
> > Cc: ITK
> > Subject: Re: [Insight-users] Compilation error with inPlace filters
> >
> >
> > Hi Radhika,
> >
> >
> > A number of changes were made last week for extending
> > the functionality of "InPlace" filters.
> >
> > You probably updated your checkout in the middle of
> > one of such modifications. Please trying cvs updating
> > to this morning (since the nightly Dashboard was quite
> > green today).
> >
> >
> > Regards,
> >
> >
> > Luis,
> >
> >
> > PS. Please don't reuse email threads with other subjects when
> > you post questions about new topics/problems. This is
> > confusing for anybody trying to follow a thread.
> >
> >
> > ---------------------------------------
> > Radhika Sivaramakrishna wrote:
> >
> > > Hi Luis,
> > > I am getting this very strange error message while compiling. Can you
> > > explain what this could be?
> > >
> > > /home/rsivaram/Insight/Code/Common/itkInPlaceImageFilter.txx: In
> member
> > > function `void itk::InPlaceImageFilter<TInputImage,
> > > TOutputImage>::AllocateOutputs() [with TInputImage = main(int,
> > > char**)::IntImageType, TOutputImage = main(int,
> > char**)::ImageType]':
> > > /home/rsivaram/Insight/Code/Common/itkImageRegion.h:173:
> > > instantiated from here
> > > /home/rsivaram/Insight/Code/Common/itkInPlaceImageFilter.txx:76: no
> > > matching
> > > function for call to `itk::InPlaceImageFilter<main(int,
> > > char**)::IntImageType, main(int,
> > > char**)::ImageType>::GraftOutput(main(int,
> > > char**)::IntImageType*)'
> > > /home/rsivaram/Insight/Code/Common/itkImageSource.txx:95: candidates
> > > are: void
> > > itk::ImageSource<TOutputImage>::GraftOutput(TOutputImage*) [with
> > > TOutputImage = main(int, char**)::ImageType]
> > >
> > >
> > > Thanks
> > > Radhika
> > >
> > >
> > >
> >
> >
> >
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