<div><font face="'courier new', monospace">I did more tests using a MR perfusion data. I chose this study because the header of each file is big ( there are a lot of private tags). </font></div><div><font face="'courier new', monospace"><br>
</font></div><div><font class="Apple-style-span" face="'courier new', monospace">I show you the 3 tests using the same data but with some differences. In the first test the codification is Little Endian Implicit, in the second one the codification is Little Endian Explicit and the last one the codification is Little Endian Explicit too but I anonymized it by Osirix in order to reduce the size of the headers since Osirix anonymization removes all private tags.</font></div>
<div><br></div><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><div><font class="Apple-style-span" face="'courier new', monospace">Mr Perfusion data test</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">======================</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace"><a href="http://dl.dropbox.com/u/3613789/perfusion_implicit_anonymized.zip">http://dl.dropbox.com/u/3613789/perfusion_implicit_anonymized.zip</a> </font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">(The test crashs when the v2.8 is used. I did the test without anonymize it)</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div><div><font class="Apple-style-span" face="'courier new', monospace">TransferSyntax: Little Endian Implicit</font></div><div><font class="Apple-style-span" face="'courier new', monospace">41,9MB</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">1080 Files</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace"> Reading directory UpdateOutputInformation UpdateLargestPossibleRegion</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">Itk 2.8 4070 9 4997</font></div><div><font class="Apple-style-span" face="'courier new', monospace">Itk 3.16 4096 13096 13655</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace">_____________________________________________</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace"><a href="http://dl.dropbox.com/u/3613789/perfusion_explicit_anonymized.zip">http://dl.dropbox.com/u/3613789/perfusion_explicit_anonymized.zip</a></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace">TransferSyntax: Little Endian Explicit</font></div><div>
<font class="Apple-style-span" face="'courier new', monospace">41,9MB</font></div><div><font class="Apple-style-span" face="'courier new', monospace">1080 Files</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div><div><font class="Apple-style-span" face="'courier new', monospace"> Reading directory UpdateOutputInformation UpdateLargestPossibleRegion</font></div><div><font class="Apple-style-span" face="'courier new', monospace">Itk 2.8 15439 32 17106</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">Itk 3.16 15510 16049 16770</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div><div><font class="Apple-style-span" face="'courier new', monospace">_______________________________________________</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><a href="http://dl.dropbox.com/u/3613789/perfusion_anonymized_osirix.zip">http://dl.dropbox.com/u/3613789/perfusion_anonymized_osirix.zip</a></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">Anonimized by Osirix. All private tags were removed.</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div><div><font class="Apple-style-span" face="'courier new', monospace">TransferSyntax: Little Endian Explicit</font></div><div><font class="Apple-style-span" face="'courier new', monospace">36,9MB</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">1080 Files</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace"> Reading directory UpdateOutputInformation UpdateLargestPossibleRegion</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">Itk 2.8 3823 8 4590</font></div><div><font class="Apple-style-span" face="'courier new', monospace">Itk 3.16 3850 4901 5332</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div></div><div><br></div>Roger<div><br>
</div><div><br><div class="gmail_quote">On Tue, Mar 23, 2010 at 4:20 AM, Bill Lorensen <span dir="ltr"><<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Brad,<br>
<br>
It looks like the meta data array is populated in both the<br>
GenerateOutputInformation and GenerateData. Also all slices are<br>
processed in GenerateOutputInformation. In 2.8, only 2 slices were<br>
processed.<br>
<br>
Why were these changes made? We are also seeing bad dicom performance<br>
in Slicer3.<br>
<br>
Bill<br>
<br>
On Mon, Mar 22, 2010 at 6:24 AM, Bradley Lowekamp<br>
<div><<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>> wrote:<br>
</div><div><div></div><div>> Hello,<br>
> Can you please tell us a little more about your test data and computer. What<br>
> kind of file system is the data on ( locale or network)? How much memory<br>
> does the computer have? What is the size of the data? What is the native<br>
> pixel type of the data? What are the actual timings? Does the execution seem<br>
> to be CPU or IO bound?<br>
> One of the changes that was made to the class was to populate the<br>
> MetaDataArray in the UpdataOutputInformation phase of the instead of the<br>
> UpdateOutputData part. This should be just reading the headers of the files<br>
> in the series. There were several reasons this change was made. To help<br>
> determine the cause of your slowness, lets break up the timing a little<br>
> further.<br>
> Could you please call:<br>
> start timer<br>
> reader->UpdateOutputInformation();<br>
> lap timer<br>
> reader->UpdateLargestPossibleRegion();<br>
> stop timer<br>
> And post the timing results.<br>
><br>
> Thanks,<br>
> Brad<br>
> On Mar 21, 2010, at 2:52 PM, Roger Bramon Feixas wrote:<br>
><br>
> This week we updated our ITK version from 2.8 to 3.16 and we noticed the<br>
> medical models are loading 2x slower using the 3.16 ITK version. We use<br>
> itk::ImageSeriesReader and the problem is focused in its Update() method.<br>
> I attached a simple test program which reproduces the problem and where we<br>
> can see that the Update() method is 2 times slower using ITK 3.16 vs. ITK<br>
> 2.8.<br>
> We compiled both versions using Visual Studio 2008 on Windows XP 32bits and<br>
> we don't known if this problem also occurs in other platforms.<br>
> I wonder if other itk users have this same performance problem and if there<br>
> is anybody can help us in order to solve it.<br>
> Thanks!<br>
><br>
> Roger<br>
> <test.zip><ATT00001..txt><br>
><br>
> ========================================================<br>
><br>
> Bradley Lowekamp<br>
><br>
> Lockheed Martin Contractor for<br>
><br>
> Office of High Performance Computing and Communications<br>
><br>
> National Library of Medicine<br>
><br>
> <a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a><br>
><br>
><br>
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