[Insight-developers] fast image pixel access method

[Gao, Yi]

Hi Kris,

My situation is actually to accelerate the sparse field level set in the
RSS segmentation module in Slicer. Their the vertex of the segmenting
surface is stored in a list. For each vertex i need to access its
neighbors. They are not purely random and they are not guaranteed to be
inside the inner region of the volume so i need the bound checking.

I will update with the list new progress on this asap i get anything new.

Thanks!

Best,
yi


On Mon, May 13, 2013 at 3:12 PM, Kris Zygmunt <krismz at sci.utah.edu> wrote:

> If you were going to take Brad's approach with generating the list of
> sample points once, you could try using the Subsamplers in
> Numerics/Statistics to do the subsampling and then use the sorts available
> in itkStatisticsAlgorithm.  You could start with
> itkUniformRandomSpatialNeighbo**rSubsampler to choose samples within a
> specified region of the image (see the corresponding test for an example).
>  In this approach, each sample is already a NeighborhoodIterator.  As Brad
> pointed out, it depends on what you're doing for this overhead to be
> useful, but I'd be curious to see how the timing works out and compars to
> what you've done already.
>
> I'm not sure whether this will be useful for you, but I mention it in case
> others are looking for ways to sample the images.
> -Kris
>
>  Date: Mon, 13 May 2013 11:59:23 -0400
>> From: Bradley Lowekamp <blowekamp at mail.nih.gov>
>> Subject: Re: [Insight-developers] fast image pixel access method
>> To: <gaoyi.cn at gmail.com>
>> Cc: "Insight-developers at itk.org" <Insight-developers at itk.org>,
>>         "Williams,      Norman K" <norman-k-williams at uiowa.edu>
>> Message-ID: <8EF7C1BA-41CE-4F5D-B7AA-**9F186F70FCE5 at mail.nih.gov<8EF7C1BA-41CE-4F5D-B7AA-9F186F70FCE5 at mail.nih.gov>
>> >
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>> One more thought.
>>
>> If you are generating the list of sample points once and then using them
>> multiple times to sample there are perhaps other interesting things which
>> could be done.
>>
>> CPU likes to access memory in a linear fashion. Depending on your
>> density, and the size of the neighborhood etc.. If you access your random
>> points in a sequential fashion you may see benefits. That is 1) generate a
>> sequential set of random points 2) sample the points in order. Step 2
>> should may see some benefits... Now under what conditions does it out
>> weight the first?
>>
>> Brad
>>
>> On May 13, 2013, at 11:49 AM, "Gao, Yi" <gaoyi.cn at gmail.com> wrote:
>>
>>  Hi Brad,
>>>
>>> Thank you for the suggestion!
>>>
>>> Sorry in my previous code I had the mistake for randomly picking
>>> position for the center point. Now I changed it to be in the inner region.
>>> index[0] = rg.lrand32(1, size[0] - 2);
>>> index[1] = rg.lrand32(1, size[1] - 2);
>>> index[2] = rg.lrand32(1, size[2] - 2);
>>>
>>> And I also turn off the boundary condition by:
>>> it.**NeedToUseBoundaryConditionOff(**);
>>>
>>> Now with the same parameters, nbhditerator is around 4 seconds (vs
>>> direct access 5.5 seconds)!
>>>
>>> I will modify my code to take advantage of this!
>>>
>>> Thank you!
>>>
>>> Best,
>>> yi
>>>
>>>
>>>
>>> On Mon, May 13, 2013 at 11:34 AM, Bradley Lowekamp <
>>> blowekamp at mail.nih.gov> wrote:
>>> Hello,
>>>
>>> On May 13, 2013, at 11:03 AM, "Gao, Yi" <gaoyi.cn at gmail.com> wrote:
>>>
>>>> When using NeighborhoodIterator, i'm not sure if the boundary checking
>>>> is automatically turned on. I guess if that is by default on, then there is
>>>> not much speed gain with it.
>>>>
>>>
>>>
>>> Because the region you specify to the Iterator is on the boundary it
>>> will turn on the boundary checking. You can either turn off the condition:
>>>
>>> http://www.itk.org/Doxygen/**html/classitk_1_**
>>> 1ConstNeighborhoodIterator.**html#**a438cb0146b802b04a771a2461952c**ff8<http://www.itk.org/Doxygen/html/classitk_1_1ConstNeighborhoodIterator.html#a438cb0146b802b04a771a2461952cff8>
>>>
>>> or you can change the region size you initialize the Iterator with.
>>>
>>> You can just use the operator<< to check what the iterator is doing.
>>>
>>> Also consider using a large type for the accumulation type, such as
>>> itk::NumericTraits<T>::**AccumulatorType;
>>>
>>> And consider using std::accumulate(it.Begin(), it.End(), 0 )
>>>
>>> Brad
>>>
>>>
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