itkantsReadWriteTransform fails if filepath contains .mat, .txt, etc. anywhere

[CGSchwarzMayo]

We ran into a confusing behavior where antsApplyTransforms would sometimes fail to read transform files, despite the file clearly existing with sufficient permissions. Upon some testing, we discovered that these same files could be read if we provided the relative, but not absolute, filepaths. The pattern turned out to be that the filepaths in question contained '.mat' inside the directory name. Specifically, we had an SGE queue named matlab.q, and /tmp files created for it were in a pattern of /tmp/.matlab.q./.

I found that itkantsReadWriteTransform.h checks for any of these strings anywhere in the filepath: .h5, .hdf5, .hdf4, .mat, .txt, .xfm. If any of these is detected anywhere in the (absolute, if given) path name of a .nii.gz transform file, it will try to read it using itk affine transform readers. These then fail, and an error is thrown, rather than attempting to use the .nii transform reading functions.

The attached patch changes this logic so that the string matching is performed only on the extension rather than the entire filepath. This could certainly be implemented in many ways, but mine copied the logic from itkTxtTransformIO.hxx using itksys::SystemTools::GetFilenameLastExtension. itksys::SystemTools is already used elsewhere in itkantsReadWriteTransform.h, so this does not introduce an extra dependency.
antsFilepathExtensionFix.txt

[CGSchwarzMayo]

diff --git a/Utilities/itkantsReadWriteTransform.h b/Utilities/itkantsReadWriteTransform.h
index 004fa8c..5377c01 100644
--- a/Utilities/itkantsReadWriteTransform.h
+++ b/Utilities/itkantsReadWriteTransform.h
@@ -40,13 +40,15 @@ ReadTransform(const std::string & filename,
   // There are known tranform type extentions that should not be considered as imaging files
   // That would be used as deformatino feilds
   // If file is an hdf5 file, assume it is a tranform instead of an image.
-  if(    filename.find(".h5")   == std::string::npos
-      && filename.find(".hdf5") == std::string::npos
-      && filename.find(".hdf4") == std::string::npos
-      && filename.find(".mat")  == std::string::npos
-      && filename.find(".txt")  == std::string::npos
-      && filename.find(".xfm")  == std::string::npos
-      )
+  bool recognizedExtension = false;
+  recognizedExtension |= ( itksys::SystemTools::GetFilenameLastExtension(filename) == ".h5" );
+  recognizedExtension |= ( itksys::SystemTools::GetFilenameLastExtension(filename) == ".hdf5" );
+  recognizedExtension |= ( itksys::SystemTools::GetFilenameLastExtension(filename) == ".hdf4" );
+  recognizedExtension |= ( itksys::SystemTools::GetFilenameLastExtension(filename) == ".mat" );
+  recognizedExtension |= ( itksys::SystemTools::GetFilenameLastExtension(filename) == ".txt" );
+  recognizedExtension |= ( itksys::SystemTools::GetFilenameLastExtension(filename) == ".xfm" );
+
+  if( !recognizedExtension )
     {
     try
       {

[stnava]

thanks - any chance you can make a pull request on github? that's the easiest way to manage and check ( automatically via travis ) + you get credit for the work, at least via a documented contribution to ants. brian

…

On Thu, Apr 12, 2018 at 4:03 PM, CGSchwarzMayo ***@***.***> wrote: We ran into a confusing behavior where antsApplyTransforms would sometimes fail to read transform files, despite the file clearly existing with sufficient permissions. Upon some testing, we discovered that these same files could be read if we provided the relative, but not absolute, filepaths. The pattern turned out to be that the filepaths in question contained '.mat' inside the directory name. Specifically, we had an SGE queue named matlab.q, and /tmp files created for it were in a pattern of /tmp/*.matlab.q.*/. I found that itkantsReadWriteTransform.h checks for any of these strings anywhere in the filepath: .h5, .hdf5, .hdf4, .mat, .txt, .xfm. If any of these is detected anywhere in the (absolute, if given) path name of a .nii.gz transform file, it will try to read it using itk affine transform readers. These then fail, and an error is thrown, rather than attempting to use the .nii transform reading functions. The attached patch changes this logic so that the string matching is performed only on the extension rather than the entire filepath. This could certainly be implemented in many ways, but mine copied the logic from itkTxtTransformIO.hxx using itksys::SystemTools::GetFilenameLastExtension. itksys::SystemTools is already used elsewhere in itkantsReadWriteTransform.h, so this does not introduce an extra dependency. antsFilepathExtensionFix.txt <https://github.com/ANTsX/ANTs/files/1904770/antsFilepathExtensionFix.txt> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#567>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AATyfqWDXRKOctDq5Ttkw_iFGEatX94Tks5tn7MggaJpZM4TSaK4> .

[CGSchwarzMayo]

You bet! I'm new to github but will figure it out.