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 <[email protected]<mailto:[email protected]>> Date: Friday, November 22, 2013 12:03 PM To: Hans Johnson <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> wrote: Seth, We discussed this at our t-con this morning. I'll try to look at it this weekend. Hans From: Seth Parker <[email protected]<mailto:[email protected]>> Date: Friday, November 22, 2013 10:09 AM To: Matt McCormick <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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" <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[email protected]> 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. ________________________________ _____________________________________ 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 ________________________________ 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. ________________________________
_______________________________________________ Powered by 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://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-developers
