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<div class=Section1>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Hello everyone,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>I was interested to see Robert's questions regarding the <span
class=SpellE>itk::SparseImage</span>. But if I understand Joshua's answer
correctly, it isn't the ideal solution. <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>I'm also interested in ways of handling the type of images that Robert
described (binary volumes with a relatively small number of "on" <span
class=SpellE>voxels</span>) and binary images in general.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Setting aside the question of whether a compression scheme is more
efficient than another for a specific type of data, I would like to know if
there are ways to store data in a certain form (not as an <span class=SpellE>itk::Image</span>)
and use them transparently with <span class=SpellE>itk</span>.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>I have the feeling that there are different levels at which the problem
can be handled:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>====================<o:p></o:p></span></font></p>
<p class=MsoPlainText><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt'>1/ Complete "solution" that allows to work
with an <span class=SpellE>itk</span> pipeline and with <span class=SpellE>iterators</span>
to access pixels directly.</span></font></span><o:p></o:p></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Ideally in this case the data never needs to be de-compressed (we never
need to re-create an <span class=SpellE>itk::Image</span>) and some intelligent
<span class=SpellE>iterators</span> are able to access a given <span
class=SpellE>voxel</span> without creating the whole <span class=SpellE>itk::Image</span>.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>====================<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>2/ Solution that allows <span class=GramE>to preserve</span> the
integrity of <span class=SpellE>itk</span> pipelines but no direct <span
class=SpellE>iterator</span> pixel access.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>In this case, filters will need to decompress the data (create an <span
class=SpellE>itk::Image</span>) temporarily, which is what a user would have to
do in order to iterate through the data.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>====================<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>3/ Solution only suitable for temporary data storage where the
"compressed" image needs to be decompressed manually every time if
access is needed (no <span class=SpellE>itk</span> pipeline support). <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>====================<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>In the following mailing list entry </span></font><st1:PersonName>Luis
Ibanez</st1:PersonName> also suggested a solution:<o:p></o:p></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>http://www.itk.org/pipermail/insight-users/2003-December/005912.html<o:p></o:p></span></font></p>
<p class=MsoPlainText><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt'>on</span></font></span> how to store the data.<o:p></o:p></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>It seems to me that one solution suggested by Luis (1-bit or RLE
compressed structure) only deals with the 3rd case. It could be however that
the other solution, using the Brains2MaskImageIO (or any IO that uses a
suitable storage scheme and can read/write in a buffer), allows storing the
data in a way that would allow propagation of update calls through the <span
class=SpellE>itk</span> pipeline (2nd case).<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>I'm not sure however whether there is an elegant solution to the first
case.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>From what I understand from Joshua's reply, <span class=SpellE>itk::SparseImage</span>
would fit in the 3rd category (is that correct?) but would have little benefit
for binary images.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>I've also noticed the existence of an <span class=SpellE>itk::Octree</span>
class, but again, I'm not sure how useful and how easy it would be to use.
Depending in the way it's implemented, it seems like it could only be used in
the 3rd case (temporary compressed data that needs to be manually un-compressed
<span class=SpellE>everytime</span> it needs to be used). But maybe it can be
adapted to fit in the 1st category? :)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Any suggestion or ideas or simply discussion on how best it would be to
tackle each “level” and/or what work’s being done on the
subject would be very welcome…<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Don’t hesitate to correct me if my understanding made me say
things that make no sense!<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Thanks<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Viet<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> Hi Robert,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> The <span class=SpellE>SparseImage</span> is a full <span
class=SpellE>itk::Image</span> of pointers which may be assigned to dynamically
allocated pixels as necessary, > and set to 0 where the image has/needs no
values.<span style='mso-spacerun:yes'> </span>Note that (1) this is only
useful when the pixel type is large > (e.g. long and/or dynamic length
feature vectors) and (2) ITK <span class=SpellE>iterator</span> and other image
manipulators do not > transparently handle this image representation, so
your code will need to explicitly manage this format. The sparse > image
class was first developed for use in a narrow band PDE solver where a
relatively large vector of values is > maintained only on pixels located in
the band.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> Josh.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> ______________________________<o:p></o:p></span></font></p>
<p class=MsoPlainText><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt'>><span style='mso-spacerun:yes'> </span>Josh</span></font></span>
Cates<span style='mso-tab-count:3'> </span><o:p></o:p></p>
<p class=MsoPlainText><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt'>><span style='mso-spacerun:yes'>
</span>Scientific</span></font></span> Computing and Imaging Institute<o:p></o:p></p>
<p class=MsoPlainText><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt'>><span style='mso-spacerun:yes'> </span></span></font></span><st1:place><st1:PlaceType><span
class=GramE>University</span></st1:PlaceType> of <st1:PlaceName>Utah</st1:PlaceName></st1:place><o:p></o:p></p>
<p class=MsoPlainText><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt'>><span style='mso-spacerun:yes'> </span></span></font></span>http://www.sci.utah.edu/~cates<o:p></o:p></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> On </span></font><st1:date Month="4" Day="5" Year="2005">Tue, 5
Apr 2005</st1:date>, Robert Maroon wrote:<o:p></o:p></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > For very large binary volumes with a relatively small<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > <span class=GramE>number of "on" <span
class=SpellE>voxels</span>, does ITK provide</span> a data<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > structure for handling this type of image in a
memory-efficient way <o:p></o:p></span></font></p>
<p class=MsoPlainText><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt'>> > (e.g., similar to <span class=SpellE>Matlab's</span>
"sparse" matrix type)?</span></font></span> Ideally, of course, <o:p></o:p></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > the fact that an image is sparse would be transparent to any<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > functions that manipulated it, and all <span class=SpellE>iterators</span>
and<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > such would function as usual.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > I found the <span class=SpellE>SparseImage</span> class, but
I'm not sure if<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > this applies (also, there's very little information<o:p></o:p></span></font></p>
<p class=MsoPlainText><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt'>> > about it on <span class=SpellE>Google</span>).</span></font></span><o:p></o:p></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > Thanks,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > Robert<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > <span style='mso-tab-count:2'> </span><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > __________________________________<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > Yahoo! Messenger <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > Show us what our next emoticon should look like. Join the
fun. <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > http://www.advision.webevents.yahoo.com/emoticontest<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > _______________________________________________<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > Insight-users mailing list<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > Insight-users@itk.org<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > http://www.itk.org/mailman/listinfo/insight-users<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> > <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> _______________________________________________<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> Insight-users mailing list<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> Insight-users@itk.org<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> http://www.itk.org/mailman/listinfo/insight-users<o:p></o:p></span></font></p>
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