WIP: ENH: Added type hints for wrapped Python classes and methods.#3
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kian-weimer wants to merge 31 commits intohjmjohnson:masterfrom
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WIP: ENH: Added type hints for wrapped Python classes and methods.#3kian-weimer wants to merge 31 commits intohjmjohnson:masterfrom
kian-weimer wants to merge 31 commits intohjmjohnson:masterfrom
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Equivalent to the existing `BSplineKernelFunction::Evaluate(u)` member function. Allows writing faster code, because it is non-virtual, and because it does not require the creation of a `BSplineKernelFunction` object.
Removed the dynamically allocated `m_Kernel` data member from `BSplineInterpolationWeightFunction` and replaced the virtual function call `m_Kernel->Evaluate(x)` by a faster static member function call, to the newly added `BSplineKernelFunction::FastEvaluate` member function. May significantly improve the performance of `BSplineInterpolationWeightFunction`.
…neKernelFunction-FastEvaluate PERF: `BSplineKernelFunction::FastEvaluate(u)`: a faster way to evaluate BSplineKernelFunction
Co-authored-by: Gabriel A. Devenyi <gdevenyi@gmail.com>
Code extracted from:
https://github.com/dzenanz/zlib-ng.git
at commit 547e8bc10654c89d3c41e1b0201fdaee35250606 (develop).
# By Zlib-ng Upstream * upstream-zlib-ng: zlib-ng 2021-09-07 (547e8bc1)
Community discussion and voting converged TransformGeometryImageFilter is a more accurate name for the operation.
Replace zlib by zlib-ng
…sformGeometryImageFilter ENH: Rename ResampleInPlaceImage to TransformGeometryImageFilter
…e-bump COMP: Bump KWStyle to address Boost warnings with GCC 11.2
Replaced `static_cast<TRealValueType>(x)` by `TRealValueType{ x }`,
following C++ Core Guidelines, August 19, 2021, "Don’t use static_cast
for arithmetic types", from
https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#Pro-type-arithmeticcast
The syntax `TRealValueType{ x }` is more type-safe than
`static_cast<TRealValueType>(x)`, as it prevents against accidental
narrowing (lossy) conversions.
Also replaced `ZeroValue()` and `OneValue()` calls by the corresponding
`TRealValueType{ x }` syntax.
Replaced `itk::Array2D` by `itk::FixedArray`, used as private `TableType` of `BSplineInterpolationWeightFunction`. This is the type of a table, used internally by its `Evaluate` member function. Declared this table `const`, and initialized the table by an in-class default-member-initializer. Defaulted the default-constructor. Follow-up to pull request InsightSoftwareConsortium#2712 commit bc7c5df "PERF: Use FixedArray for BSplineBaseTransform ParameterIndexArrayType" commit 9bf745b "PERF: Use FixedArray for BSplineInterpolationWeightFunction OutputType"
It should be replaced by std::enable_if from STL.
…rapping Avoid build errors when we wrap for 4-D images.
…ray-dimensions-4 BUG: Improve dimension-dependent BSplineInterpolationWeightFunction wrapping
GCC is not resolving `object->Superclass` in some cases even though the definition is available and other compilers are resolving the definition. xref InsightSoftwareConsortium#2676
Add named pipeline inputs of InputImage and RigidTransform and use macro to provide standard class methods from named inputs. Removed unneeded m_OutputImage member variable.
The TransformGeometryImageFilter::GenerateData method was refactored for correct pipeline behavior. The output Image's meta-data is correctly modifed in the GenerateOutputInformation method, so that down stream filters can uses the information. The composite pipeline is not isolated from the inputs and output using the double graft convention. However, only the bulk data pointer and buffered region are copied to the output, as not to change the geometry information previously set.
Enable not copying the input image's bulk pixel data by default.
Replace TransformGeometryImageFilter::SetRigidTransform with SetTransform, while adding support for generic linear transform. The Transform::ApplyToImageMetadata method is re-used for computation.
…geometry-superclass COMP: Avoid Superclass type alias GCC compile errors
Some functionality has been moved to the igenerator.py file. This code will add typehinting for all methods ran through the `generate_method` method. Several C++ types are converted to their Python equavelent but many more still need to be converted.
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hjmjohnson
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Nov 7, 2021
…n metric Fix uninitialized variable use in `ANTS` neighborhood correlation metric: ensure that `fixedImageGradient` and `movingImageGradient` have valid values before assigning them to the `scanMem` struct that scans over images. Fixes: ``` Run-Time Check Failure #3 - The variable 'fixedImageGradient' is being used without being initialized. ``` The bug was affecting a number of tests in the `ITKRegistrationMethodsv4Test` module. Signaled at https://open.cdash.org/viewTest.php?onlyfailed&buildid=7067466 and https://open.cdash.org/viewTest.php?onlyfailed&buildid=7069241
hjmjohnson
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Nov 11, 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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This PR is a work in progress designed to produce class, method, and parameter type typehints for all ITK classes (or as many as possible).
While the current implementation works in general, there are many edge cases that are not yet covered.
This PR currently includes several ITK commits that have occurred recently.