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Hi,
<div class=""><br class="">
</div>
<div class="">I was initially wondering the magnitude of the difference, but this should not be a problem for this algorithm.</div>
<div class="">Looking at the algorithm a little closer, I see it is computed mostly by counting voxel and intercepts ( not with floating point operations ), so the results should be extremely numerically stable and not subject to accumulation error. </div>
<div class=""><br class="">
</div>
<div class="">It would be good to find a reproducible and shareable case. That is can you share a small image where the problem occours? Hopefully it can be reproduced by just reading it and running BinaryImageToShapLabelMapFilter.</div>
<div class=""><br class="">
</div>
<div class="">Do you know if the release or debug state is correct?</div>
<div class=""><br class="">
</div>
<div class="">To roll out a threading issue, can you set ITK to use only one thread, with the env variable ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1, or itk::MultiThreader::SetGlobalDefaultNumberOfThread(1) and see if the problem persists?</div>
<div class=""><br class="">
</div>
<div class="">If the problem persists with one thread then, add a debug message to this method [1], to print the label ID and number of intercepts for each axis. This should be the same.</div>
<div class=""><br class="">
</div>
<div class="">HTH,</div>
<div class="">Brad</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkShapeLabelMapFilter.hxx#L633" class="">https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkShapeLabelMapFilter.hxx#L633</a></div>
<div class=""><br class="">
</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On May 13, 2016, at 3:12 PM, ebasafa <<a href="mailto:ehsan.basafa@gmail.com" class="">ehsan.basafa@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Thank
you! The IJ article is really helpful.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">However,
the issue still remains that debug and release give different</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">answers.
I do not know what specifics I need to provide. Basically, I have a</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">pipeline
that loads a volume from file, thresholds the image into a binary</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">image,
and then passes it to BinaryImageToShapeLabelMapFilter to process all</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">the
objects found after thresholding. The exact same pipeline, run over the</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">same
image volume, prints out different values for perimeter and roundness</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">of
the same objects. I should have mentioned that I am working in 3D, and</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">also
the values I get for other shape parameters, e.g. flatness, elongation,</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">equivalent
ellipsoid radii, volume, etc. are the same for debug and release.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">My
very naive guess is that, possibly, there is some uninitialized parameter</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">being
used somewhere in the filter, which results in debug and release</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">initializing
it to two different values.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Lowekamp,
Bradley (NIH/NLM/LHC) [C] wrote</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
Hello,<br class="">
<br class="">
You can find additional information about how this parameter is defined in<br class="">
the following insight journal:<br class="">
<a href="http://www.insight-journal.org/browse/publication/852" class="">http://www.insight-journal.org/browse/publication/852</a><br class="">
<br class="">
This method is generalizable to N-D, so it may not be the most accurate in<br class="">
2D. The method can produce roundness numbers that are >1. However is<br class="">
should be consistent in debug and release modes. Getting consistent<br class="">
numeric computation with C++ and vectorizable operations can be<br class="">
challenging with different architectures.<br class="">
<br class="">
You did not provide any specifics for the difference in computation<br class="">
between release and debug modes.<br class="">
<br class="">
HTH,<br class="">
Brad<br class="">
<br class="">
<blockquote type="cite" class="">On May 13, 2016, at 11:26 AM, ebasafa <<br class="">
</blockquote>
</blockquote>
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
ehsan.basafa@<br class="">
</blockquote>
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
> wrote:<br class="">
<blockquote type="cite" class=""><br class="">
Hi everyone,<br class="">
<br class="">
Recently I noticed that BinaryImageToShapeLabelMapFilter does not<br class="">
calculate<br class="">
roundness of objects correctly, and I traced it back to perimeter<br class="">
calculation. More curiously, the results I get from the GetRoundness()<br class="">
and<br class="">
GetPerimeter() methods differ between debug and release builds! And to<br class="">
make<br class="">
it even more confusing, it's a machine-dependent problem, i.e. on some<br class="">
machines debug and release give the same (correct?) numbers and on some<br class="">
machines they don't. I suspect that release results are erroneous, since<br class="">
some roundness numbers turn out to be >1.0 in release but are always <1.0<br class="">
in<br class="">
debug mode. I am working in a Windows 8.1 64-bit environment and am using<br class="">
the latest release of ITK (4.9.1) on all different machines.<br class="">
<br class="">
I have tried several searches to see if this is a resolved issue, but the<br class="">
latest post I found was from 2011 (link below) and has been unanswered.<span class="Apple-converted-space"> </span><br class="">
<br class="">
<a href="http://itk-users.7.n7.nabble.com/Perimeter-Calculation-via-LabelImageToShapeLabelMapFilter-td14917.html" class="">http://itk-users.7.n7.nabble.com/Perimeter-Calculation-via-LabelImageToShapeLabelMapFilter-td14917.html</a><br class="">
<br class="">
Seems like there was a bug report filed that time<br class="">
(<a href="https://itk.org/Bug/view.php?id=11934" class="">https://itk.org/Bug/view.php?id=11934</a>) whose status still says<br class="">
"assigned".<br class="">
I appreciate any help.<br class="">
<br class="">
Thanks,<br class="">
Ehsan<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
--<br class="">
View this message in context:<br class="">
<a href="http://itk-insight-users.2283740.n2.nabble.com/ShapeLabelMap-Roundness-Perimeter-Calculation-Issue-tp7588837.html" class="">http://itk-insight-users.2283740.n2.nabble.com/ShapeLabelMap-Roundness-Perimeter-Calculation-Issue-tp7588837.html</a><br class="">
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<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Lowekamp,
Bradley (NIH/NLM/LHC) [C] wrote</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
Hello,<br class="">
<br class="">
You can find additional information about how this parameter is defined in<br class="">
the following insight journal:<br class="">
<a href="http://www.insight-journal.org/browse/publication/852" class="">http://www.insight-journal.org/browse/publication/852</a><br class="">
<br class="">
This method is generalizable to N-D, so it may not be the most accurate in<br class="">
2D. The method can produce roundness numbers that are >1. However is<br class="">
should be consistent in debug and release modes. Getting consistent<br class="">
numeric computation with C++ and vectorizable operations can be<br class="">
challenging with different architectures.<br class="">
<br class="">
You did not provide any specifics for the difference in computation<br class="">
between release and debug modes.<br class="">
<br class="">
HTH,<br class="">
Brad<br class="">
<br class="">
<blockquote type="cite" class="">On May 13, 2016, at 11:26 AM, ebasafa <<br class="">
</blockquote>
</blockquote>
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ehsan.basafa@<br class="">
</blockquote>
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> wrote:<br class="">
<blockquote type="cite" class=""><br class="">
Hi everyone,<br class="">
<br class="">
Recently I noticed that BinaryImageToShapeLabelMapFilter does not<br class="">
calculate<br class="">
roundness of objects correctly, and I traced it back to perimeter<br class="">
calculation. More curiously, the results I get from the GetRoundness()<br class="">
and<br class="">
GetPerimeter() methods differ between debug and release builds! And to<br class="">
make<br class="">
it even more confusing, it's a machine-dependent problem, i.e. on some<br class="">
machines debug and release give the same (correct?) numbers and on some<br class="">
machines they don't. I suspect that release results are erroneous, since<br class="">
some roundness numbers turn out to be >1.0 in release but are always <1.0<br class="">
in<br class="">
debug mode. I am working in a Windows 8.1 64-bit environment and am using<br class="">
the latest release of ITK (4.9.1) on all different machines.<br class="">
<br class="">
I have tried several searches to see if this is a resolved issue, but the<br class="">
latest post I found was from 2011 (link below) and has been unanswered.<span class="Apple-converted-space"> </span><br class="">
<br class="">
<a href="http://itk-users.7.n7.nabble.com/Perimeter-Calculation-via-LabelImageToShapeLabelMapFilter-td14917.html" class="">http://itk-users.7.n7.nabble.com/Perimeter-Calculation-via-LabelImageToShapeLabelMapFilter-td14917.html</a><br class="">
<br class="">
Seems like there was a bug report filed that time<br class="">
(<a href="https://itk.org/Bug/view.php?id=11934" class="">https://itk.org/Bug/view.php?id=11934</a>) whose status still says<br class="">
"assigned".<br class="">
I appreciate any help.<br class="">
<br class="">
Thanks,<br class="">
Ehsan<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
--<br class="">
View this message in context:<br class="">
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