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

Seth Parker csparker247 at gmail.com
Mon Nov 25 09:26:24 EST 2013 

That is a major difference in how I understood registration was working. Is
the origin adding issue something that comes about because of my landmark
selection? Or have I really stumbled upon a bug?

*Seth Parker*
Video Editor | The University of Kentucky Vis Center
www.csethparker.com | www.vis.uky.edu


On Fri, Nov 22, 2013 at 4:35 PM, Johnson, Hans J <hans-johnson at uiowa.edu>wrote:

>  Seth,
>
>  Registration is done in PHYSICAL space, not pixel space.  I think the
> problems you are running into
>
>  PhysicalSpace = DirectionCos*Spacing*PixelIndex+Origin
>
>  The previous bug is that “Spacing” was not being interpreted properly
> for JPEG images.  Based on your image, it appears as if perhaps you now
> have an “origin” adding problem.
>
>  Hans
>
>   From: Seth Parker <csparker247 at gmail.com>
> Date: Friday, November 22, 2013 at 3:30 PM
> To: "insight-users at itk.org" <insight-users at itk.org>, Hans Johnson <
> hans-johnson at uiowa.edu>
> Subject: Fwd: [Insight-users] [ITK Community] Problem with
> LandmarkWarping2.cxx in ITK-4.4.0?
>
>   Realized this got sent to insight-dev's which I'm not a part of, so it
> bounced it back. Forwarding so that it's tracked in insight-users.
>
>  ---------- Forwarded message ----------
> From: Seth Parker <csparker247 at gmail.com>
> Date: Fri, Nov 22, 2013 at 3:49 PM
> Subject: Re: [Insight-users] [ITK Community] Problem with
> LandmarkWarping2.cxx in ITK-4.4.0?
> To: "Johnson, Hans J" <hans-johnson at uiowa.edu>
> Cc: Luis Ibanez <luis.ibanez at kitware.com>, ITK <insight-developers at itk.org
> >
>
>
> You'll have to forgive me; I'm a video editor by trade and have been at a
> steep learning curve to get this far into the troubleshooting. Let me make
> sure I understand. Essentially, the disparate ppi's in my images are
> causing my issue. If, just by example, all of my images were set to the
> same ppi, things should work correctly. My use of JPEGs caused the
> difference of outputs that I was interpreting as correct behavior.
>
> Assuming this is the concept, I went back and ran a test from my original
> TIF images (they're in the 100MB range so I wasn't using them before). I
> changed everything to 72 ppi in Photoshop without resampling so that every
> image had the same dimensions as before, then ran LandmarkWarping2 again.
> This time, 4.3.2 and 4.4.0 did produce the same output, but it didn't
> produce a correct output, at least not how I understand Landmark Warping
> should work. This is what that output yielded:
> https://dl.dropboxusercontent.com/u/13015285/Chad-4.4.0-005.jpg (Note:
> This is a jpeg made from the output tif, just to cut down on filesize).
>
> It seems as if the output is at the appropriate scale, but it obviously is
> not in the expected spot. Am I just missing something in the concept of
> landmark warping, did I not understand that voxel spacing concept, or is
> there something else going on?
>
> Thank you all so much for your help. I'm going to try the suggested
> "SetOutputParameters" change, too, to see what happens.
>
> *Seth Parker*
> Video Editor | The University of Kentucky Vis Center
> www.csethparker.com | www.vis.uky.edu
>
>
>   On Fri, Nov 22, 2013 at 2:10 PM, Johnson, Hans J <hans-johnson at uiowa.edu
> > wrote:
>
>>  Luis:  THANK YOU FOR LOOKING INTO THIS!
>> Seth:  I think you were depending on a "bug" in the JPEGIO code to get
>> the desired behavior you wanted.
>>  ===============
>>
>>  As an experiment, if you convert each of your images to tif format and
>> run the 4.3.2 version of the code, you will have consistent results with
>> both ITK4.3.2 and ITK4.4.0.
>>
>>  1-StaticImage.jpg*   <-- 5412 × 7216 pixels, 304.79 pixels/inch
>> 2-MovingImage.jpg* <-- 4800 × 5434 pixels, 72 pixels/inch
>> LandmarkWarped-ITK4.3.2.jpg <-- 5412 × 7216 pixels, 72 pixels/inch
>> LandmarkWarped-ITK4.4.0.jpg  <-- 5412 × 7216 pixels, 72 pixels/inch
>>
>>  For the resampling stage of the output you are propagating the input
>> image voxel counts, but not the input image voxel spacings.
>>
>>  My guess is that you want to use "SetOutputParametersFromImage(const
>> ImageBaseType *image);" and pass the input image for your call to the
>> "itk::ResampleImageFilter".
>>
>>  This will result in an output image with the same pixels/inch as your
>> input image.
>>
>>  Hans
>>
>>
>>   From: Luis Ibanez <luis.ibanez at kitware.com>
>> Date: Friday, November 22, 2013 12:03 PM
>> To: Hans Johnson <hans-johnson at uiowa.edu>
>>
>> Subject: Re: [Insight-users] [ITK Community] Problem with
>> LandmarkWarping2.cxx in ITK-4.4.0?
>>
>>   Hans,
>>
>>  Here is what I found:
>>
>>  aleph $ git bisect bad
>>
>>  Bisecting: 0 revisions left to test after this (roughly 0 steps)
>> [b7c71079a70b33a4018e132b31ee2fc0a36b8129] ENH: JPEG IO now writes and
>> reads spacing, similar to the TIFF IO (ITK-3023)
>> aleph $ git log --oneline -1
>> b7c7107 ENH: JPEG IO now writes and reads spacing, similar to the TIFF IO
>> (ITK-3023)
>>
>>
>>  aleph $ git bisect bad
>>
>>
>>  b7c71079a70b33a4018e132b31ee2fc0a36b8129 is the first bad commit
>>
>>
>>  commit b7c71079a70b33a4018e132b31ee2fc0a36b8129
>> Author: Marco Feuerstein <marco.feuerstein at gmail.com>
>> Date:   Tue Apr 30 12:01:29 2013 +0200
>>
>>      ENH: JPEG IO now writes and reads spacing, similar to the TIFF IO
>> (ITK-3023)
>>
>>     Change-Id: I5f40e226040233672eed3dcdec1a5b9007899574
>>
>>  :040000 040000 61ddc795f11d33660d4aba2c5d74059256b0ab6f
>> c3402b325c2329b6ab88919270e0b98b70402c0d MModules
>>
>>
>>
>>  So, it seems that the problem is not with the Landmark Deformation
>> itself,
>> but
>> with the fact that we now put spacing information in the resulting output
>> jpg image.
>>
>>
>> https://github.com/Kitware/ITK/commit/b7c71079a70b33a4018e132b31ee2fc0a36b8129
>>
>>
>>     Luis
>>
>>
>>
>> On Fri, Nov 22, 2013 at 12:26 PM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
>>
>>> Hans,
>>>
>>>  I'm playing with the git bisect, while I sit in long meetings...
>>> I'm making progress (5 steps to go).
>>>
>>>  Will let you know how far I get.
>>>
>>>     Thanks
>>>
>>>        Luis
>>>
>>>
>>> On Fri, Nov 22, 2013 at 11:11 AM, Johnson, Hans J <
>>> hans-johnson at uiowa.edu> wrote:
>>>
>>>>  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>
>>>> Date: Friday, November 22, 2013 10:09 AM
>>>> To: Matt McCormick <matt.mccormick at kitware.com>
>>>> Cc: "insight-users at itk.org" <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 | 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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