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

Fri Nov 22 11:09:35 EST 2013

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 | www.vis.uky.edu

On Thu, Nov 21, 2013 at 4:51 PM, Matt McCormick
<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>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 | www.vis.uky.edu
>>
>>
>> On Wed, Nov 20, 2013 at 9:04 PM, Bradley Lowekamp <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> 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> 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> 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 | www.vis.uky.edu
>>>>  _____________________________________
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>>>>
>>>
>>
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