<div dir="ltr"><div>ok, i will use statistics.<br></div>How could I wrapp ITK histogram calculator to simpleitk?<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/5/7 Bradley Lowekamp <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hello,<div><br><div>ITK proper has a very nice framework for creating new thresholds based on histograms contributed by Richard Beare and Gaetan Lehmann in the Insight Journal[1]. In SimpleITK the ~dozen filters[2] which use this framework are available[3].</div>
<div><br></div><div>It may be reasonable to crate a new ITK histogram calculator and matching threshold filter, then add the new json wrapping to SimpleITK.</div><div><br></div><div>So these methods, are a global threshold, not a connected threshold. However, if you run a global threshold followed by a connected component algorithm you can get the same result by choosing a selected component. For large images with large components this can be more computation efficient, and both the global threshold and connected components methods are efficiently multi-threaded.</div>
<div><br></div><div>I have also used the Statistics[3] and LabelStatistics[3] image filters to compute thresholds based on certain standard deviations. I have also computed certain robust nth-order statistics with numpy by getting access to image buffer. Unfortunately, this buffer access method is not available in Java yet. There is likely just a little bit of SWIG code that is needed, and some TESTS written. We aiming to get some community support to put some sugar on top for many of the languages that SimpleITK supports. So there have been a couple of discussions on the mailing list regarding this interface.</div>
<div><br></div><div>There are quite a number of options you have. Please let me know if need any additional info deciding what is best for you or help getting started.</div><div><br></div><div>Brad</div><div><br></div><div>
[1] <a href="http://hdl.handle.net/10380/3279" target="_blank">http://hdl.handle.net/10380/3279</a></div><div>[2] <a href="http://www.itk.org/Doxygen/html/group__ITKThresholding.html" target="_blank">http://www.itk.org/Doxygen/html/group__ITKThresholding.html</a></div>
<div>[3] <a href="http://www.itk.org/SimpleITKDoxygen/html/annotated.html" target="_blank">http://www.itk.org/SimpleITKDoxygen/html/annotated.html</a></div><div>[4] <a href="http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1StatisticsImageFilter.html" target="_blank">http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1StatisticsImageFilter.html</a></div>
<div>[5] <a href="http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1LabelStatisticsImageFilter.html" target="_blank">http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1LabelStatisticsImageFilter.html</a></div>
<div><div class="h5"><div><br></div><div><br></div><div><div><div>On May 7, 2013, at 7:55 AM, Thibault Varacca <<a href="mailto:thibault.varacca@gmail.com" target="_blank">thibault.varacca@gmail.com</a>> wrote:</div>
<br><blockquote type="cite"><div dir="ltr"><div>Yes, i'm using JAVA and my volumes are 32 bit float value.<br></div>I want to use an histogram to set automaticaly the lower and upper values of the connectedthresholdfilter that i use later.<br>
</div>
<div class="gmail_extra"><br><br><div class="gmail_quote">2013/5/7 Bradley Lowekamp <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hello,<div><br></div><div>SimpleITK does not have the Statistics module wrapped.</div><div><br></div><div>What language are you using with SimpleITK? I have just been using numpy's histogram functionality from python when needed.</div>
<div><br></div><div>The AdaptiveHistogramEqualizationImageFilter is a way to vary the intensity of an image so that in a local region of each pixel the histogram has a certain shape. This can be done for local contrast enhancement and similar effects.</div>
<div><br></div><div>Brad</div><div><div><div><br></div><div><br></div><div><br><div><div>On May 7, 2013, at 7:44 AM, Thibault Varacca <<a href="mailto:thibault.varacca@gmail.com" target="_blank">thibault.varacca@gmail.com</a>> wrote:</div>
<br><blockquote type="cite"><div dir="ltr"><div>But using simpleITK, I juste have AdaptiveHistogramEqualizationImageFilter() ... Do you know how it works? I didn't really understand the description.<br></div>Regards<br>
</div><div class="gmail_extra">
<br><br><div class="gmail_quote">2013/5/7 Thibault Varacca <span dir="ltr"><<a href="mailto:thibault.varacca@gmail.com" target="_blank">thibault.varacca@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Thank you Parseval :)<br></div><div class="gmail_extra"><div><br><br><div class="gmail_quote">2013/5/7 parseval <span dir="ltr"><<a href="mailto:cabkai@web.de" target="_blank">cabkai@web.de</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
in "<Itk-Folder>\Examples\Statistics\"<br>
you can find several examples of ImageHistograms#.cxx.<br>
ITK doesn't restrict an image to be 2D. Therefore you can simply modify the<br>
examples for 3D case.<br>
<br>
best,<br>
Parseval<br>
<br>
<br>
<br>
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