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<p class=Standard>Hi Karthik,<o:p></o:p></p>
<p class=Standard><o:p> </o:p></p>
<p class=Standard>thanks <span lang=EN-US>for</span><span lang=EN-US> </span><span
lang=EN-US>your</span><span lang=EN-US> </span><span lang=EN-US>reply</span>. <span
lang=EN-US>I share your performance concerns, if you use the PolygonSpatialObjects
for the VOI processing. I hoped a scene-graph like VOI structure allows me to
process just the image regions specified for a specific question without much
effort, by just picking the desired object/object node from the tree. But the
isInside processing gets quite slow if you select for instance the tree node for
several VOIs. If think, if I just convert my structure data to an ImageMaskSpatialObject
I wouldn’t be so flexible (and the conversion would take more time). But I
will keep your suggestion in mind, if the performance isn’t acceptable I will
have to change the implementation.<o:p></o:p></span></p>
<p class=Standard><span lang=EN-US><o:p> </o:p></span></p>
<p class=Standard><span lang=EN-US>Best regards<o:p></o:p></span></p>
<p class=Standard><span lang=EN-US>Andreas<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Von:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
insight-users-bounces@itk.org [mailto:insight-users-bounces@itk.org] <b>Im
Auftrag von </b>Karthik Krishnan<br>
<b>Gesendet:</b> Dienstag, 13. Juli 2010 13:56<br>
<b>An:</b> Jäger Andreas<br>
<b>Cc:</b> Insight-users; Insight Developers<br>
<b>Betreff:</b> Re: [Insight-users] Image mask and SpatialObjects<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'>Thanks for pointing this out. I agree
with all your observations. I'm not sure what the correct solution is. My guess
is that most of us have used the mask spatial objects of the form (a)
ImageMaskSpatialObject with masked images (b) EllipsoidSpatialObject with an
approximate ellipsoid defining the brain (c) BoxSpatialObject, with a cuboid
ROI on the target image. </span><br>
<br>
For RTStruct data, we've converted them to ImageMaskSpatialObject and then used
them; because it simply did not seem to be a reasonable thing to represent them
as PolygonSpatialObject, given how slow the IsInside() becomes. One has to do
the line based voting against every polygon boundary point; and do this for
every pixel and transformed pixel; and at do this at every iteration. The
marginally improved precision of representing the ROI as a mesh may not to be worth
the time.<br>
<br>
Thanks<br>
--<br>
karthik<o:p></o:p></p>
<div>
<p class=MsoNormal>On Tue, Jul 13, 2010 at 2:24 PM, Jäger Andreas <<a
href="mailto:A.Jaeger@dkfz-heidelberg.de">A.Jaeger@dkfz-heidelberg.de</a>>
wrote:<o:p></o:p></p>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>Hi,</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>i had a problem concerning the usage of SpatialObjects (e.g.
GroupSpatialObjects, ContourSpatialObjects, SpatialObjectTreeContainer,
PolygonGroupSpatialObjects, PolygonSpatialObjects...) to mask a specific image
for the registration.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>I think there are probably other people doing similar stuff, and
there could be interest in discussing a few implementation decisions concerning
SpatialObject child classes and the way the MeanSquaresImageToImageMetric is
processing them.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>I use PolygonGroupSpatialObjects and PolygonSpatialObjects to create
my own Volumes of Interest and Contours out of a set of points.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>I use these two SpatialObject types, because a)i import proprietary
structure data, which is not pixel based (Thats the reason why I don't use
ImageMaskSpatialObject for instance).</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> b)the MeanSquaresImageToImageMetric is not working with any
other combination of SpatialObject I tried so far (at least for the way i nest
SpatialObjects).</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>I store the Contours in PolygonSpatialObjects and store all contours
of a VOI in PolygonGroupSpatialObjects.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>The Tree SpatialObject for all VOIs is also a
PolygonGroupSpatialObject.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>As mentioned they are actually the only classes I can use,
that’s why I wanted to discuss the implementation of a few other
SpatialObject classes.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>For better understanding, here a part of my test program in
pseudocode :</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>create StructureLoader</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>create RegistrationAlgorithm</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>RegistrationAlgorithm->SetFixedImg()</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>RegistrationAlgorithm->SetMovingImg()</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>RegistrationAlgorithm->SetTargetMask(StrucureLoader->getStructure())
// returns the generated tree node object</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>RegistrationAlgorithm->GetRegistration() </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>The program delivers correct values(when trying to determine which
image regios are inside/outside the mask) only,</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>if I use the PolygonGroupSpatialObjects for nodes(voi and voi
groups) and the PolygonSpatialObjects for leaves(contours).</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>While trying to understand, why my implementation was not working as
planned with other SpacialObject classes (e.g. GroupSpatialObjects,
ContourSpatialObjects), I noticed several implementation decisions,</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>which are responsible for the unexpected behavior.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>I have a few questions concerning the implementation of
A)MeanSquaresImageToImageMetric::GetValueAndDerivative(...)/GroupSpatialObject::IsInside(...)</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> B)PolygonSpatialObject::IsInside(...)/PolygonGroupSpatialObject::IsInside(...)</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>and hope that someone is able to explain them to me.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> A)</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> The MeanSquaresImageToImageMetric::GetValueAndDerivative()
calls the IsInside() method without a parameter for the depth</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> Line 178: if( this->m_FixedImageMask &&
!this->m_FixedImageMask->IsInside( inputPoint ) )</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> which has the effect that for all SpatialObject classes(at
least as far as i know) the default depth=0 is used.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> --> Was this implementation done with respect to the usage
of SpatialObjects?</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> I would assume if someone who is using SpatialObject would
probably like to use the feature of creating tree like structures by nesting
objects,</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> but actually there are not many SpatialObjects which really
check for existing childern, and rather use a depth = 0 as default?</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> e.g. GroupSpatialObjects (i think this class is a good
example, because you would expect a different behavior)</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> GroupSpatialObject has no own implementation of IsInside()</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> So the IsInside() Method checks as follows</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> if( depth > 0 )</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> {</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> do something</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> }</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> else </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> return false</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> --> reasonable you always get false, when
MeanSquaresImageToImageMetric::GetValueAndDerivative(...) checks the points of
the image!</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> Wouldn't it make more sense not to use the default IsInside
implementation, because assuming a default depth=0 for GroupSpatialObjects
seems to make no real sense.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> I can't really imagine, why someone should use a
GroupSpatialObject with a depth of zero (for instance there could be a check of
the childrenList if depth = 0 is passed).</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> This is actually one reason why I use
PolygonGroupSpatialObjects, because it was the only class I could find, which
assumes it has children.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> I didn't check other metrics so far, so i don't know if they
behave the same way.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> B)</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> For testing purposes I wanted to use only one contour of a
VOI, for faster processing</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> pseudocode:</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> RegistrationAlgorithm->setTargetMask(structureLoader.getContourSpatialObject()->GetFirstVOI()->GetFirstContour());</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> I noticed, that if you use a PolygonSpecialObject without a
PolygonGroupSpatialObjects, you get wrong return values for IsInside(),</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> because there is no z-dimension check in the
PolygonSpecialObject::IsInside(...) method.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> So if s.o. directly calls the PolygonSpecialObject::IsInside()
method, he gets true for the points even if they are in an other plane than the
polygon.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> this behavour forces you to use a PolygonGroupSpatialObject
even if you would just have 1 PolygonSpecialObject inside.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> Can someone explain me, why PolygonSpecialObject was
implemented that way? I think it is quite cofusing for someone, who works with
theses classes the first time, because IsInside just doesn't behave as you
would expect.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> compare itkPolygonSpatialObject.txx Line 403-485</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>If I take a look at how MeanSquaresImageToImageMetric is using the
IsInside() method, and the way method is implemented in the different classes,
I somehow miss the "thread" in the way the parts are designed.</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US>But perhaps I just don't get the concept, I would appreciate it if
someone could elucidate it for me ;). If someone thinks the way I build my
Structures is a unfavorable solution, hints and tips are always welcome!</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
lang=EN-US> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Best
regards<o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Andreas<o:p></o:p></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'><br>
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