[Insight-developers] Coordinate system semantics of ImageIOBase?

[Steve M. Robbins]

On Sun, Jan 11, 2009 at 09:30:47PM -0500, Rupert Brooks wrote:

> 2 - larger problem: popen   popen is not standard on windows, but your
> CreateMincFile.h uses it.
> Ultimately this is a sidetrack issue, as its just being used for the
> testing. However, it blocked
> me from compiling your test suite for the moment.

Yes, I suspected this would be a problem.  I probably should have
highlighted it.  I can think of two ways around this issue.  First, we
could generate a set of files like Andrew and you did; the trick is
that there will be a lot of them.  The second idea is to use MINC
directly to create the files rather than using popen() to pipe the
data into "rawtominc" as I am doing.  If I were to code it, I'd
probably go for the second option.


> 3 -boost issues - i had trouble getting FIND_PACKAGE(Boost to work
> properly.

Whoa!  I ditched Boost after learning about Googletest, so there
should not be any FIND_PACKAGE(Boost) stuff.  Are you speaking of the
attachment "testmincio-smr.tar.gz" from bug #6038
http://www.itk.org/Bug/view.php?id=6038 ?


> Just a couple questions:
> 

> MINC and ITK use different ways of specifying the origin / offset of
> the coordinate system.  I believe
> that MINC uses the xstart, ystart, zstart as the distance _along the
> x,y,z direction cosines_, while
> ITK places the origin _such that pixel 0,0,0 is at the origin_.

If that's true, then it is my misunderstanding.

Since ImageIOBase::GetOrigin() is not documented, I asked this list
about it:

ME:
> The method GetOrigin(int i) returns a double; I assume that
> GetOrigin(0), GetOrigin(1), GetOrigin(2) return the column,
> row, and slice, respectively, of the world-space origin.
> Is that correct?
> 

Louis responded "Yes"; c.f.
http://www.itk.org/mailman/private/insight-developers/2008-December/011435.html

To me, that means that ITK's GetOrigin() is the same notion as MINC's
"starts".  If these are not identical, then I need a better description
of what GetOrigin() returns.


> If the spacing is negative (legal in MINC) then the direction cosine
> gets flipped.  Good so far, but Isn't it also necessary
> to either flip the image in memory, or shift the origin to the other
> end of the negative axis?

I worried a bit about that, but I'm not certain of the answer.  I
hadn't gotten that far in the coding.


Thanks for inspecting the code,
-Steve
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