[Insight-users] [ITK Community] Problem with LandmarkWarping2.cxx in ITK-4.4.0?

Fri Nov 22 11:11:33 EST 2013

Seth,

We discussed this at our t-con this morning.  I'll try to look at it this weekend.

Hans

From: Seth Parker <csparker247 at gmail.com<mailto:csparker247 at gmail.com>>
Date: Friday, November 22, 2013 10:09 AM
To: Matt McCormick <matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>>
Cc: "insight-users at itk.org<mailto:insight-users at itk.org>" <insight-users at itk.org<mailto:insight-users at itk.org>>
Subject: Re: [Insight-users] [ITK Community] Problem with LandmarkWarping2.cxx in ITK-4.4.0?

I had to rebuild ITK as I don't think the tests were built unless I also included the cmake flag ITK_BUILD_ALL_MODULES. Maybe not. Anyway, I ran the LandmarkWarping test and it reported that it passed. I would be inclined to think that there was something just wrong with my landmarks file if it weren't for the fact that the exact same file produces expected results on an older version.

Seth Parker
Video Editor | The University of Kentucky Vis Center
www.csethparker.com<http://www.csethparker.com> | www.vis.uky.edu<http://www.vis.uky.edu>

On Thu, Nov 21, 2013 at 4:51 PM, Matt McCormick <matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>> wrote:
Hi Seth,

To run the test associated with the examples, set

  BUILD_EXAMPLES  ON

in the ITK CMake configuration, build, and run

  ctest -R LandmarkWarping

on the command line in the ITK build directory.

Thanks,
Matt

On Thu, Nov 21, 2013 at 4:20 PM, Seth Parker <csparker247 at gmail.com<mailto:csparker247 at gmail.com>> wrote:
Ok, so a couple of updates. First, I checked and I had tested on Ubuntu 13.04 (Raring Ringtail) and had compiled using GCC 4.7.3. ITK 4.4.0 gave me the same issues with LandmarkWarping2 as on OSX.

On OSX, I had never noticed that Xcode's gcc was using an llvm backend. Clang is supposedly the same way. Also, I've already update all of our computers to OSX 10.9 as we hardly ever do any ITK or development work, so going back to Mountain Lion isn't really an option. However, I did spend today compiling GNU GCC (4.8.2) on my machine and I recompiled ITK 4.4.0 using it instead of Xcode's "GCC". After a successful build, it also exhibits the same issue with LandmarkWarping2. I'm not sure of other variables, but I think it's safe to assume this isn't a compiler issue.

In terms of using the built-in tests, I can find one LandmarkWarping2Test.png under the testing data, but I'm unclear on which of the other images I should register it against (or against it).

Seth Parker
Video Editor | The University of Kentucky Vis Center
www.csethparker.com<http://www.csethparker.com> | www.vis.uky.edu<http://www.vis.uky.edu>

On Wed, Nov 20, 2013 at 9:04 PM, Bradley Lowekamp <brad at lowekamp.net<mailto:brad at lowekamp.net>> wrote:
Hello,

I am just curious if it's a compiler issue or one with the code.

It's been a while since there has been a bonified version of GNU GCC with Xcode. I am running OS 10.8.5, check this out:

$ /usr/bin/gcc -v
Using built-in specs.
Target: i686-apple-darwin11
Configured with: /private/var/tmp/llvmgcc42/llvmgcc42-2336.11~182/src/configure --disable-checking --enable-werror --prefix=/Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2 --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-prefix=llvm- --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin11 --enable-llvm=/private/var/tmp/llvmgcc42/llvmgcc42-2336.11~182/dst-llvmCore/Developer/usr/local --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11 --target=i686-apple-darwin11 --with-gxx-include-dir=/usr/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)

That is llvm masquerading as gcc.

There is also clang as an option. I'd give that a try. Upgrading to Macericks is going to another set of problems.

Check out the information here:
http://public.kitware.com/pipermail/community/2013-November/000188.html

This may be a good opportunity to run git-bisect, if the issue can be reproduced.

Brad

On Nov 20, 2013, at 8:57 PM, Seth Parker <csparker247 at gmail.com<mailto:csparker247 at gmail.com>> wrote:

I did try on Ubuntu (Raring Ringtail). It's been a while for Ubuntu, but I believe I used gcc for it. Definitely gcc on OSX. I haven't tried recompiling since upgrading to Mavericks, but I was running Mountain Lion before and Xcode 4.6.

It hadn't occurred to me to check the built-in examples. I should be able to test that tomorrow.

Sent from my phone

On Nov 20, 2013 8:27 PM, "Bradley Lowekamp" <brad at lowekamp.net<mailto:brad at lowekamp.net>> wrote:
Hello,

Have you tried other systems? Linux perhaps?

What compiler are you using? What OS? What XCode version?

Is this issue reproducible with a test or example already in ITK?

Thanks,
Brad

On Nov 20, 2013, at 4:02 PM, Seth Parker <csparker247 at gmail.com<mailto:csparker247 at gmail.com>> wrote:

Was attempting to use ITK-4.4.0 LandmarkWarping2 on OSX and was getting completely incorrect results. The moving image was roughly in the correct spot of the first landmark, but was at a completely incorrect scale. I reverted to 4.3.2 and had no issues at all. I'm fine using 4.3.2, but thought I would mention it here in case anyone has a solution or pointer.

You can download examples of the input and output files here: https://dl.dropboxusercontent.com/u/13015285/LandmarkWarping.zip

Seth Parker
Video Editor | The University of Kentucky Vis Center
www.csethparker.com<http://www.csethparker.com/> | www.vis.uky.edu<http://www.vis.uky.edu/>
_____________________________________
Powered by www.kitware.com<http://www.kitware.com/>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://www.itk.org/mailman/listinfo/insight-users

_____________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://www.itk.org/mailman/listinfo/insight-users

_______________________________________________
Community mailing list
Community at itk.org<mailto:Community at itk.org>
http://public.kitware.com/cgi-bin/mailman/listinfo/community

________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
________________________________
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20131122/d44cbdc8/attachment.htm>