[Insight-developers] Get/SetPixel() with taking an offsetparameter
Miller, James V (GE, Research)
millerjv at crd.ge.com
Tue Dec 19 16:48:52 EST 2006
Wrt to the std::map< PixelType, std::vector< IndexType > >, I have thought about this a few times and always verred away because of the memory requirements.
If we are adopting these high memory implementations, we may want to have an option to switch to a lower memory albeit slower version.
I just had a thought that maybe some of these algorithms that use a map as above could be done in several iterations. Less than the number of pixel intensity values but more than one. Say you divide the intensity space into k bands, say you build the map with the top 10% of the pixels, then do whatever processing you can do, then build the map with the next 10%, etc.
-----Original Message-----
From: insight-developers-bounces+millerjv=crd.ge.com at itk.org [mailto:insight-developers-bounces+millerjv=crd.ge.com at itk.org] On Behalf Of Gaetan Lehmann
Sent: Tuesday, December 12, 2006 6:13 AM
To: Luis Ibanez
Cc: insight-developers at itk.org
Subject: Re: [Insight-developers] Get/SetPixel() with taking an offsetparameter
Hi,
>
> Hi Gaetan,
>
> That's an interesting option.
>
> However, please note that a better way of approaching this problem is
> to create an Iterator that is specific to the way you want to walk in
> your image.
>
> It seems that in your algorithm you are already defining a clever way
> of finding the offsets that will lead you to the next pixel of
> interest. What we probably want to explore is the possibility of
> creating a new Image Iterator that will do the equivalent job.
>
What is done in ReconstructionByDilationImageFilter currently work only with shape iterators, so having the same operators on the other iterators would be great. I'm not sure that a dedicated iterator is needed.
> In general you want to avoid having direct access to the image buffer.
> One of the reasons for it is that soon we will be introducing in ITK
> an alternative memory layout where the pixel data is not stored in a
> contiguous block of memory. Instead, the pixel data may be stored as a
> collection of disconnected slices.
>
> Having a GetPixel()/SetPixel() methods with direct access to the
> buffer data will not work in this memory layout. We already will have
> to manage the modification of the existing ComputOffset() method.
>
I'm not sure that modifying the Get/SetPixel() method is the best way to go, but what is proposed has no extra cost, because the ComputeIndex() and
ComputeOffset() are already exposed, and there is nothing more done that using these methods.
> You will also have a harder time making sure that the algorithm works
> in N-Dimensional images. It is in general, easier, to delegate to
> Iterators the complex details of dealing with the N-Dimensionality of
> the image.
It will not be harder, because an iterator is used to get the offsets :-) Offsets are only a cheaper representation of Index, and the conversion can be easily done with the ComputeIndex() and ComputeOffset() methods.
>
> What is the specific way in which you need to walk through the image
> in the morphological reconstruction filters that you are preparing ?
>
A common step - at least common enough to make me implement it several
times - is to sort the pixels by there value to process the highest value
first for example. The data structure used to do that is:
std::map< PixelType, std::vector< IndexType > >
after have filled this data structure with all the pixels in the image,
it's easy to process all the pixels in the image in the right order.
If we take care of the memory allocation of the vectors (which require an
extra iteration step), for a big image (1024 x 1024 x 80), this structure
take about 1024*1024*80*4*3/1024^2 = 960 MB on a 32 bits system - twice
more a 64bits one. When using offsets, the cost is reduced by the image
dimension, 3 in that case = 320 MB. The difference is quite significant :-)
This example is "only" an optimization problem, as the pixels can be
processed in the right order without that, by iterating over the image as
many time as we have pixel values in the image (and one more time to find
the maximum).
The next case is more difficult.
The component tree representation (also called min tree or max tree) don't
store the image in a array, but in a tree of connected components in the
image. All the nodes of that tree are associated to a list of pixels in
the image - a list of itk::Index. That's no more an algorithm
optimization, but a data representation problem, and the itk way of
designing a pixel location make it highly inefficient compared to what can
be done in other image analysis libs.
It is already possible to use offsets instead of itk::Index. That's what
I'm doing in the component trees, for memory efficiency (please, don't
make the ComputeOffset() and ComputeIndex() method deprecated !). However,
the permanent conversion itk::Index <-> offset seem to be an important
extra cost which should be avoided.
I have not measured the extra cost of the conversion, so perhaps I'm
wrong, and the conversion cost is not significant compared to the rest of
the algorithms.
Given the comments about performance in the code, I think that the
measures of the execution time of those conversion have already been done.
Can you give a pointer to those results ?
Thanks,
Gaetan
>
> Please let us know,
>
>
> Thanks
>
>
> Luis
>
>
>
> ----------------------
> Gaetan Lehmann wrote:
>> Hi,
>> Currently, the GetPixel() and SetPixel() methods of the itk::Image
>> class are taking a itk::Index parameter to know which pixel is
>> concerned in the image.
>> The itk::Image also have the ComputeIndex() and ComputeOffset() methods
>> to manipulate directly the offset in the buffer, and to convert this
>> offset from/to an index.
>> Manipulating indexes in an algorithm (like in the current
>> morphological reconstruction filters, in the component tree
>> contribution I'm preparing
>> (http://voxel.jouy.inra.fr/darcsweb/darcsweb.cgi?r=componentTree;a=summary),
>> ...) would be a lot more efficient, both in memory and in execution
>> time, by using the offsets instead of the indexes: store an itk::Index
>> cost 3 long (with dim=3), while an offset is only 1, and there is no
>> need to convert the offset to an index and the index to an offset.
>> Unfortunately, there is no Get/SetPixel() method able to work with an
>> offset.
>> I think that it would be a good idea to implement them as follow (not
>> tested yet, that's an example):
>> in itkImage.h:
>> void SetPixel(const OffsetValueType &offset, const TPixel& value)
>> {
>> (*m_Buffer)[offset] = value;
>> }
>> const TPixel& GetPixel(const OffsetValueType &offset) const
>> {
>> return ( (*m_Buffer)[offset] );
>> }
>> TPixel& GetPixel(const OffsetValueType &offset)
>> {
>> return ( (*m_Buffer)[offset] );
>> }
>> TPixel & operator[](const OffsetValueType &offset)
>> { return this->GetPixel(offset); }
>> const TPixel& operator[](const OffsetValueType &offset) const
>> { return this->GetPixel(offset); }
>> void SetPixel(const IndexType &index, const TPixel& value)
>> {
>> typename Superclass::OffsetValueType offset =
>> this->ComputeOffset(index);
>> this->SetPixel( offset, value );
>> }
>> const TPixel& GetPixel(const IndexType &index) const
>> {
>> typename Superclass::OffsetValueType offset =
>> this->ComputeOffset(index);
>> return this->GetPixel( offset );
>> }
>> TPixel& GetPixel(const IndexType &index)
>> {
>> typename Superclass::OffsetValueType offset =
>> this->ComputeOffset(index);
>> return this->GetPixel( offset );
>> }
>> TPixel & operator[](const IndexType &index)
>> { return this->GetPixel(index); }
>> const TPixel& operator[](const IndexType &index) const
>> { return this->GetPixel(index); }
>> in itkImageAdaptor.h:
>> void SetPixel(const IndexType &index, const PixelType & value)
>> { m_PixelAccessor.Set( m_Image->GetPixel(index), value ); }
>> PixelType GetPixel(const IndexType &index) const
>> { return m_PixelAccessor.Get( m_Image->GetPixel(index) ); }
>> PixelType operator[](const IndexType &index) const
>> { return m_PixelAccessor.Get( m_Image->GetPixel(index) ); }
>> void SetPixel(const OffsetValueType &offset, const PixelType & value)
>> { m_PixelAccessor.Set( m_Image->GetPixel(offset), value ); }
>> PixelType GetPixel(const OffsetValueType &offset) const
>> { return m_PixelAccessor.Get( m_Image->GetPixel(offset) ); }
>> PixelType operator[](const OffsetValueType &offset) const
>> { return m_PixelAccessor.Get( m_Image->GetPixel(offset) ); }
>> Does it seem reasonable to do that ?
>> Thanks,
>> Gaetan
>>
--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr
_______________________________________________
Insight-developers mailing list
Insight-developers at itk.org
http://www.itk.org/mailman/listinfo/insight-developers
More information about the Insight-developers
mailing list