DOC: Fix copy/paste error in description of itkFactorylessNewMacro #1
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kwrobot
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May 22, 2014
A temporary jacobian value was always created for and resized at every iteration of the program call. This was increadibly in-efficient during registrations and was the #1 time consuming portion of the code for many registration examples. The new function: ComputeJacobianWithRespectToParametersCachedTemporaries was created to allow for improved performance. Change-Id: Ic405b9d26c5fdf3660941372e9bb9814c2792143
kwrobot
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Jul 21, 2014
From Coverity: CID 1175336 (#1 of 1): Unchecked dynamic_cast (FORWARD_NULL) 4. var_deref_model: Passing null pointer "optimizer" to function "itk::RegularStepGradientDescentBaseOptimizer::GetCurrentIteration() const", which dereferences it. (The dereference happens because this is a virtual function call.) Change-Id: Ie49596c0db7b413f37cdce4bb2332360f535588e
kwrobot
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Dec 17, 2015
…tern". This commit updates explicit instantiation to use "extern" keyword similarly to what was done in InsightSoftwareConsortium/ITK@b72726c (BUG: Explicitly instantiate common MetaDataObjects). By using the recommended approach for template instantiation, this commit should also fix TransformReadWriteTest where TransformIO failed to be successfully instantiated. Here is the error that was reported when the was compiled on MacOSX using clang-6.0: libc++abi.dylib: terminating with uncaught exception of type itk::ExceptionObject: /scratch/dashboards/MacOSX-clang6/ITK/Modules/IO/TransformBase/src/itkTransformFileWriterSpecializations.cxx:212: itk::ERROR: TransformFileWriterTemplate(0x7fa552100f10): The input of writer should be whether a double precision or a single precision transform type. Called from TransformFileWriterTemplate<double,double$ It also updates IOTransformDCMTK remote module to include a similar fix. Note #1: To shut up the following warning from gcc, context specific "pragma GCC diagnostic" preprocessor instructions have been added: warning: type attributes ignored after type is already defined [-Wattributes] This is most likely specific to gcc (see issue #39159), and at the time of this commit there were no resolution or information about gcc version where the "problem" is addressed. See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=39159 For that reason, the "pragma GCC diagnostic" is applied in-conditionally of the gcc version being used. Note #2: While "extern" is only part of the c++ standard starting with c++11 (see section 14.7.2 of the standard), it is supported by Visual Studio 2008, GCC and Clang using compiler specific extension in earlier version: * Visual Studio 2008: https://msdn.microsoft.com/en-us/library/by56e477(v=vs.90).aspx * Gcc: https://gcc.gnu.org/onlinedocs/gcc-4.8.4/gcc/Template-Instantiation.html#Template-Instantiation * Clang (since v2.9): http://clang.llvm.org/cxx_status.html For completeness, initial draft of the "extern" keyword were first introduced in 2003 [1] and then revised in 2006 [2], and ultimately standardized in c++11 [3]: [1] N1448: http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2003/n1448.pdf [2] N1987: http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2006/n1987.htm [3] N3242: http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2011/ See InsightSoftwareConsortium#3393 Suggested-by: Bradley Lowekamp <blowekamp@mail.nih.gov> Co-authored-by: Bradley Lowekamp <blowekamp@mail.nih.gov> Change-Id: I2e3ca2843c500b9bb60bbffc5f3629bc5be0a6fd
kwrobot
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Apr 25, 2017
Allow external modules to be reported about the values the ITK BUILD_EXAMPLES and BUILD_DOCUMENTATION flags have so that building their own examples and documentation can be dependent on the general ITK options. This patch is motivated by the discussion about PR #1 in https://github.com/InsightSoftwareConsortium/ITKPrincipalComponentAnalysis Change-Id: Ib829b9c7fcde4568888f08b4bba09d9e1a2f7431
kwrobot
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Aug 15, 2017
Bradley Lowekamp (7):
BUG: Always request the full input image
ENH: replace run-time check of dimension with concept check
ENH: Prefer raw pointers in pipeline methods
ENH: Prefer FillBuffer over iterator loop
ENH: Remove unneeded negative input
COMP: Fix warning about variable index being shadowed
Merge pull request #3 from blowekamp/FixShadowWarning
Francois Budin (2):
Merge pull request #1 from
blowekamp/PipelineFixesAndImprovements
Merge pull request #2 from blowekamp/Improvements
Change-Id: Ica14efa46f5ee2ef7d38ab9b22999f69f98b3eb6
kwrobot
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Aug 17, 2017
Bradley Lowekamp (7):
BUG: Always request the full input image
ENH: replace run-time check of dimension with concept check
ENH: Prefer raw pointers in pipeline methods
ENH: Prefer FillBuffer over iterator loop
ENH: Remove unneeded negative input
COMP: Fix warning about variable index being shadowed
Merge pull request #3 from blowekamp/FixShadowWarning
Francois Budin (2):
Merge pull request #1 from
blowekamp/PipelineFixesAndImprovements
Merge pull request #2 from blowekamp/Improvements
Change-Id: Ica14efa46f5ee2ef7d38ab9b22999f69f98b3eb6
kwrobot
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Mar 21, 2024
In 03c8176 a concept check was added that the sobel operator uses a signed pixel type. On Linux aarch64, ❯ c++ --version c++ (Debian 12.2.0-14) 12.2.0 ❯ uname -a Linux deb 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux char is unsigned, which causes the concept check to fail. Switch `char` to `signed char`.
kwrobot
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Apr 29, 2024
Found with thread sanitizer (TSan) running the `itkANTSNeighborhoodCorrelationImageToImageRegistrationTest` unit test.
There was already a `m_ANTSAssociateOnceFlag` flag for use with `std::call_once`, so I just used that in this place too (it's already used elsewhere).
Partial backtrace from TSan:
```
WARNING: ThreadSanitizer: data race (pid=79176)
Write of size 8 at 0x000108f02240 by thread T2:
#0 void itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution_impl<itk::ThreadedIndexedContainerPartitioner>(itk::IdentityHelper<itk::ThreadedIndexedContainerPartitioner>, itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:118 (ITKMetricsv4TestDriver:arm64+0x1004bfe50)
#1 itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution(itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h:235 (ITKMetricsv4TestDriver:arm64+0x1004bf9c0)
#2 itk::DomainThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreaderCallback(void*) itkDomainThreader.hxx:123 (ITKMetricsv4TestDriver:arm64+0x100259b6c)
#3 std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()::operator()() const itkThreadPool.h:92 (ITKMetricsv4TestDriver:arm64+0x1007d3228)
#4 decltype(std::declval<void* (*&)(void*)>()(std::declval<itk::PoolMultiThreader::ThreadPoolInfoStruct*>())) std::__1::__invoke[abi:v160006]<std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()&>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&) invoke.h:394 (ITKMetricsv4TestDriver:arm64+0x1007d31a4)
Previous write of size 8 at 0x000108f02240 by thread T14:
#0 void itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution_impl<itk::ThreadedIndexedContainerPartitioner>(itk::IdentityHelper<itk::ThreadedIndexedContainerPartitioner>, itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:118 (ITKMetricsv4TestDriver:arm64+0x1004bfe50)
#1 itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution(itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h:235 (ITKMetricsv4TestDriver:arm64+0x1004bf9c0)
#2 itk::DomainThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreaderCallback(void*) itkDomainThreader.hxx:123 (ITKMetricsv4TestDriver:arm64+0x100259b6c)
#3 std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()::operator()() const itkThreadPool.h:92 (ITKMetricsv4TestDriver:arm64+0x1007d3228)
#4 decltype(std::declval<void* (*&)(void*)>()(std::declval<itk::PoolMultiThreader::ThreadPoolInfoStruct*>())) std::__1::__invoke[abi:v160006]<std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()&>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&) invoke.h:394 (ITKMetricsv4TestDriver:arm64+0x1007d31a4)
```
kwrobot
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May 30, 2024
Found with thread sanitizer (TSan) running the `itkANTSNeighborhoodCorrelationImageToImageRegistrationTest` unit test.
There was already a `m_ANTSAssociateOnceFlag` flag for use with `std::call_once`, so I just used that in this place too (it's already used elsewhere).
Partial backtrace from TSan:
```
WARNING: ThreadSanitizer: data race (pid=79176)
Write of size 8 at 0x000108f02240 by thread T2:
#0 void itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution_impl<itk::ThreadedIndexedContainerPartitioner>(itk::IdentityHelper<itk::ThreadedIndexedContainerPartitioner>, itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:118 (ITKMetricsv4TestDriver:arm64+0x1004bfe50)
#1 itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution(itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h:235 (ITKMetricsv4TestDriver:arm64+0x1004bf9c0)
#2 itk::DomainThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreaderCallback(void*) itkDomainThreader.hxx:123 (ITKMetricsv4TestDriver:arm64+0x100259b6c)
#3 std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()::operator()() const itkThreadPool.h:92 (ITKMetricsv4TestDriver:arm64+0x1007d3228)
#4 decltype(std::declval<void* (*&)(void*)>()(std::declval<itk::PoolMultiThreader::ThreadPoolInfoStruct*>())) std::__1::__invoke[abi:v160006]<std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()&>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&) invoke.h:394 (ITKMetricsv4TestDriver:arm64+0x1007d31a4)
Previous write of size 8 at 0x000108f02240 by thread T14:
#0 void itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution_impl<itk::ThreadedIndexedContainerPartitioner>(itk::IdentityHelper<itk::ThreadedIndexedContainerPartitioner>, itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:118 (ITKMetricsv4TestDriver:arm64+0x1004bfe50)
#1 itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution(itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h:235 (ITKMetricsv4TestDriver:arm64+0x1004bf9c0)
#2 itk::DomainThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreaderCallback(void*) itkDomainThreader.hxx:123 (ITKMetricsv4TestDriver:arm64+0x100259b6c)
#3 std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()::operator()() const itkThreadPool.h:92 (ITKMetricsv4TestDriver:arm64+0x1007d3228)
#4 decltype(std::declval<void* (*&)(void*)>()(std::declval<itk::PoolMultiThreader::ThreadPoolInfoStruct*>())) std::__1::__invoke[abi:v160006]<std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()&>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&) invoke.h:394 (ITKMetricsv4TestDriver:arm64+0x1007d31a4)
```
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