[Insight-developers] Best way to concatenate itk Arrays?

[Luis Ibanez]

Hi Michael,

On Fri, Dec 10, 2010 at 1:37 PM, Michael Stauffer (Circular Logic)
<mstauff at verizon.net> wrote:
> Thanks Luis, that sounds good.
>
> Digger deeper I see actually that vnl_vector::copy_out is just using a
> for loop to copy by element, so that's no advantage. What a tease! :)
>

Yeap,

You must always go down to the Source code to find the truth   :-)


> Following Nick's use of data_block in BSplineDeformableTransform, I see
> that ImportImageContainer ends up calling memcpy with this data pointer.
> So it seems that's kosher for me to use too? Ill try that.
>

we use memcpy in several places,
so that seems to be compatible.

> I'm not sure how STL would help me here (presumably you meant
> containers?). Seems it might involve more copying than a direct memcpy
> from Array to another Array.
>

Yeap, I meant STL containers.
sorry for not being specific.

greping in the STL headers, it looks like the valarray maps
to memcpy (or at least a built-in version of it).  This may or
may not help for what you have in mind....

Note that there is a cautionary message:

  // For non-fundamental types, it is wrong to say 'memcpy()'

We use Valarray in

ITK/Code/Common/itkValarrayImageContainer.h

that is our default pixel container.

In other words: by default the pixel buffer of ITK images
is stored in a std::valarray.

...but I don't know if that relates to the functionality
that you are implementing...


    Luis



-----------
> -M
>
>>-----Original Message-----
>>From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
>>Sent: Friday, December 10, 2010 12:22 PM
>>To: Michael Stauffer (Circular Logic)
>>Cc: Nicholas Tustison; ITK-dev-list
>>Subject: Re: [Insight-developers] Best way to concatenate itk Arrays?
>>
>>Hi Michael,
>>
>>As long as the vnl code is not exposed in the ITK API,
>>it should be fine.
>>
>>(...we have some places where this rule has note been
>>respected and probably should clean them up...).
>>
>>You are also free to use STL inside the implementation
>>code, if you find that useful for this case.
>>
>>
>>     Luis
>>
>>
>>-------------------------------------
>>On Thu, Dec 9, 2010 at 5:43 PM, Michael Stauffer (Circular Logic)
>><mstauff at verizon.net> wrote:
>>> Thanks Nick. This is what I've used so far, along with
>>copy_out(). I was
>>> checking to see if it's Kosher with itk best practices, since it's
>>> relying on the underlying data type.
>>>
>>> Cheers,
>>> Michael
>>>
>>>>-----Original Message-----
>>>>From: Nicholas Tustison [mailto:ntustison at gmail.com]
>>>>Sent: Thursday, December 09, 2010 4:38 PM
>>>>To: Michael Stauffer (Circular Logic)
>>>>Cc: 'ITK-dev-list'
>>>>Subject: Re: [Insight-developers] Best way to concatenate itk Arrays?
>>>>
>>>>Hi Michael,
>>>>
>>>>You should look in the BSplineDeformableTransform class where
>>>>the data_block() function is accessed directly.
>>>>
>>>>Nick
>>>>
>>>>
>>>>On Dec 9, 2010, at 4:18 PM, Michael Stauffer (Circular Logic) wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I need to concatenate itk Arrays (Transform::ParameterType objects,
>>>>> actually) into a single new Array. Is it acceptable to
>>>>directly use the
>>>>> underlying public vnl_vector routines like data_block() and
>>>>copy_out()
>>>>> to do this efficiently? Or must I copy element-by-element using
>>>>> Array::GetElement(). Or is there some other way I'm missing?
>>>>>
>>>>> I could add an Insert method to Array that allows inserting
>>>>of another
>>>>> array at a given index, in order to avoid using the
>>>>vnl_vector routines
>>>>> directly.
>>>>>
>>>>> This is part of the new CompositeTransform class. We're set-ing and
>>>>> get-ing concatenated parameter arrays that hold the
>>>>parameters for all
>>>>> the constituent transforms in the composite class. We may
>>>>have dozens of
>>>>> transforms at once, so element-by-element copying will start
>>>>to add up
>>>>> over all the calls to get and set parameters made by the
>>optimizer in
>>>>> the registration process.
>>>>>
>>>>> Cheers,
>>>>> Michael
>>>>>
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