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Add spatial options to thresh and cyl option to clip (#1281)
* add cyl to clip, working on spatial opts for thresh * more thresh wiring * wip * add geom ext fix patch to spack build * wire up tests for thresh implicit func cases * fix typo * remove unneeded header * thresh dont support inverted plane * wire up invert option to field threshold case * container with patched vtk-m * update containers
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145 changes: 145 additions & 0 deletions
145
scripts/build_ascent/2024_05_03_vtkm-mr3215-ext-geom-fix.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,145 @@ | ||
| From 49518e5054c607942f644c82a5289e12b0f50476 Mon Sep 17 00:00:00 2001 | ||
| From: Kenneth Moreland <morelandkd@ornl.gov> | ||
| Date: Fri, 3 May 2024 09:22:56 -0400 | ||
| Subject: [PATCH] Fix bug with ExtractGeometry filter | ||
|
|
||
| The `ExtractGeometry` filter was outputing datasets containing | ||
| `CellSetPermutation` as the representation for the cells. Although this is | ||
| technically correct and a very fast implementation, it is essentially | ||
| useless. The problem is that any downstream processing will have to know | ||
| that the data has a `CellSetPermutation`. None do (because the permutation | ||
| can be on any other cell set type, which creates an explosion of possible | ||
| cell types). | ||
|
|
||
| Like was done with `Threshold` a while ago, this problem is fixed by deep | ||
| copying the result into a `CellSetExplicit`. This behavior is consistent | ||
| with VTK. | ||
| --- | ||
| .../changelog/extract-geometry-permutation.md | 13 +++++++ | ||
| .../testing/UnitTestExtractGeometryFilter.cxx | 13 ++++++- | ||
| .../worklet/ExtractGeometry.h | 34 +++++++------------ | ||
| 3 files changed, 37 insertions(+), 23 deletions(-) | ||
| create mode 100644 docs/changelog/extract-geometry-permutation.md | ||
|
|
||
| diff --git a/docs/changelog/extract-geometry-permutation.md b/docs/changelog/extract-geometry-permutation.md | ||
| new file mode 100644 | ||
| index 0000000000..8a90495f76 | ||
| --- /dev/null | ||
| +++ b/docs/changelog/extract-geometry-permutation.md | ||
| @@ -0,0 +1,13 @@ | ||
| +# Fix bug with ExtractGeometry filter | ||
| + | ||
| +The `ExtractGeometry` filter was outputing datasets containing | ||
| +`CellSetPermutation` as the representation for the cells. Although this is | ||
| +technically correct and a very fast implementation, it is essentially | ||
| +useless. The problem is that any downstream processing will have to know | ||
| +that the data has a `CellSetPermutation`. None do (because the permutation | ||
| +can be on any other cell set type, which creates an explosion of possible | ||
| +cell types). | ||
| + | ||
| +Like was done with `Threshold` a while ago, this problem is fixed by deep | ||
| +copying the result into a `CellSetExplicit`. This behavior is consistent | ||
| +with VTK. | ||
| diff --git a/vtkm/filter/entity_extraction/testing/UnitTestExtractGeometryFilter.cxx b/vtkm/filter/entity_extraction/testing/UnitTestExtractGeometryFilter.cxx | ||
| index 675df8f77c..14de333666 100644 | ||
| --- a/vtkm/filter/entity_extraction/testing/UnitTestExtractGeometryFilter.cxx | ||
| +++ b/vtkm/filter/entity_extraction/testing/UnitTestExtractGeometryFilter.cxx | ||
| @@ -11,6 +11,7 @@ | ||
| #include <vtkm/cont/testing/MakeTestDataSet.h> | ||
| #include <vtkm/cont/testing/Testing.h> | ||
|
|
||
| +#include <vtkm/filter/clean_grid/CleanGrid.h> | ||
| #include <vtkm/filter/entity_extraction/ExtractGeometry.h> | ||
|
|
||
| using vtkm::cont::testing::MakeTestDataSet; | ||
| @@ -41,11 +42,21 @@ public: | ||
| vtkm::cont::DataSet output = extractGeometry.Execute(dataset); | ||
| VTKM_TEST_ASSERT(test_equal(output.GetNumberOfCells(), 8), "Wrong result for ExtractGeometry"); | ||
|
|
||
| + vtkm::filter::clean_grid::CleanGrid cleanGrid; | ||
| + cleanGrid.SetCompactPointFields(true); | ||
| + cleanGrid.SetMergePoints(false); | ||
| + vtkm::cont::DataSet cleanOutput = cleanGrid.Execute(output); | ||
| + | ||
| vtkm::cont::ArrayHandle<vtkm::Float32> outCellData; | ||
| - output.GetField("cellvar").GetData().AsArrayHandle(outCellData); | ||
| + cleanOutput.GetField("cellvar").GetData().AsArrayHandle(outCellData); | ||
|
|
||
| VTKM_TEST_ASSERT(outCellData.ReadPortal().Get(0) == 21.f, "Wrong cell field data"); | ||
| VTKM_TEST_ASSERT(outCellData.ReadPortal().Get(7) == 42.f, "Wrong cell field data"); | ||
| + | ||
| + vtkm::cont::ArrayHandle<vtkm::Float32> outPointData; | ||
| + cleanOutput.GetField("pointvar").GetData().AsArrayHandle(outPointData); | ||
| + VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(0) == 99); | ||
| + VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(7) == 90); | ||
| } | ||
|
|
||
| static void TestUniformByBox1() | ||
| diff --git a/vtkm/filter/entity_extraction/worklet/ExtractGeometry.h b/vtkm/filter/entity_extraction/worklet/ExtractGeometry.h | ||
| index 97521335f2..449d7eae60 100644 | ||
| --- a/vtkm/filter/entity_extraction/worklet/ExtractGeometry.h | ||
| +++ b/vtkm/filter/entity_extraction/worklet/ExtractGeometry.h | ||
| @@ -10,11 +10,13 @@ | ||
| #ifndef vtkm_m_worklet_ExtractGeometry_h | ||
| #define vtkm_m_worklet_ExtractGeometry_h | ||
|
|
||
| +#include <vtkm/worklet/CellDeepCopy.h> | ||
| #include <vtkm/worklet/WorkletMapTopology.h> | ||
|
|
||
| #include <vtkm/cont/Algorithm.h> | ||
| #include <vtkm/cont/ArrayCopy.h> | ||
| #include <vtkm/cont/ArrayHandle.h> | ||
| +#include <vtkm/cont/CellSetExplicit.h> | ||
| #include <vtkm/cont/CellSetPermutation.h> | ||
| #include <vtkm/cont/CoordinateSystem.h> | ||
| #include <vtkm/cont/Invoker.h> | ||
| @@ -114,28 +116,13 @@ public: | ||
| } | ||
| }; | ||
|
|
||
| - //////////////////////////////////////////////////////////////////////////////////// | ||
| - // Extract cells by ids permutes input data | ||
| - template <typename CellSetType> | ||
| - vtkm::cont::CellSetPermutation<CellSetType> Run(const CellSetType& cellSet, | ||
| - const vtkm::cont::ArrayHandle<vtkm::Id>& cellIds) | ||
| - { | ||
| - using OutputType = vtkm::cont::CellSetPermutation<CellSetType>; | ||
| - | ||
| - vtkm::cont::ArrayCopy(cellIds, this->ValidCellIds); | ||
| - | ||
| - return OutputType(this->ValidCellIds, cellSet); | ||
| - } | ||
| - | ||
| - //////////////////////////////////////////////////////////////////////////////////// | ||
| - // Extract cells by implicit function permutes input data | ||
| template <typename CellSetType, typename ImplicitFunction> | ||
| - vtkm::cont::CellSetPermutation<CellSetType> Run(const CellSetType& cellSet, | ||
| - const vtkm::cont::CoordinateSystem& coordinates, | ||
| - const ImplicitFunction& implicitFunction, | ||
| - bool extractInside, | ||
| - bool extractBoundaryCells, | ||
| - bool extractOnlyBoundaryCells) | ||
| + vtkm::cont::CellSetExplicit<> Run(const CellSetType& cellSet, | ||
| + const vtkm::cont::CoordinateSystem& coordinates, | ||
| + const ImplicitFunction& implicitFunction, | ||
| + bool extractInside, | ||
| + bool extractBoundaryCells, | ||
| + bool extractOnlyBoundaryCells) | ||
| { | ||
| // Worklet output will be a boolean passFlag array | ||
| vtkm::cont::ArrayHandle<bool> passFlags; | ||
| @@ -149,7 +136,10 @@ public: | ||
| vtkm::cont::Algorithm::CopyIf(indices, passFlags, this->ValidCellIds); | ||
|
|
||
| // generate the cellset | ||
| - return vtkm::cont::CellSetPermutation<CellSetType>(this->ValidCellIds, cellSet); | ||
| + vtkm::cont::CellSetPermutation<CellSetType> permutedCellSet(this->ValidCellIds, cellSet); | ||
| + | ||
| + vtkm::cont::CellSetExplicit<> outputCells; | ||
| + return vtkm::worklet::CellDeepCopy::Run(permutedCellSet); | ||
| } | ||
|
|
||
| vtkm::cont::ArrayHandle<vtkm::Id> GetValidCellIds() const { return this->ValidCellIds; } | ||
| -- | ||
| GitLab | ||
|
|
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145 changes: 145 additions & 0 deletions
145
scripts/uberenv_configs/packages/vtk-m/2024_05_03_vtkm-mr3215-ext-geom-fix.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,145 @@ | ||
| From 49518e5054c607942f644c82a5289e12b0f50476 Mon Sep 17 00:00:00 2001 | ||
| From: Kenneth Moreland <morelandkd@ornl.gov> | ||
| Date: Fri, 3 May 2024 09:22:56 -0400 | ||
| Subject: [PATCH] Fix bug with ExtractGeometry filter | ||
|
|
||
| The `ExtractGeometry` filter was outputing datasets containing | ||
| `CellSetPermutation` as the representation for the cells. Although this is | ||
| technically correct and a very fast implementation, it is essentially | ||
| useless. The problem is that any downstream processing will have to know | ||
| that the data has a `CellSetPermutation`. None do (because the permutation | ||
| can be on any other cell set type, which creates an explosion of possible | ||
| cell types). | ||
|
|
||
| Like was done with `Threshold` a while ago, this problem is fixed by deep | ||
| copying the result into a `CellSetExplicit`. This behavior is consistent | ||
| with VTK. | ||
| --- | ||
| .../changelog/extract-geometry-permutation.md | 13 +++++++ | ||
| .../testing/UnitTestExtractGeometryFilter.cxx | 13 ++++++- | ||
| .../worklet/ExtractGeometry.h | 34 +++++++------------ | ||
| 3 files changed, 37 insertions(+), 23 deletions(-) | ||
| create mode 100644 docs/changelog/extract-geometry-permutation.md | ||
|
|
||
| diff --git a/docs/changelog/extract-geometry-permutation.md b/docs/changelog/extract-geometry-permutation.md | ||
| new file mode 100644 | ||
| index 0000000000..8a90495f76 | ||
| --- /dev/null | ||
| +++ b/docs/changelog/extract-geometry-permutation.md | ||
| @@ -0,0 +1,13 @@ | ||
| +# Fix bug with ExtractGeometry filter | ||
| + | ||
| +The `ExtractGeometry` filter was outputing datasets containing | ||
| +`CellSetPermutation` as the representation for the cells. Although this is | ||
| +technically correct and a very fast implementation, it is essentially | ||
| +useless. The problem is that any downstream processing will have to know | ||
| +that the data has a `CellSetPermutation`. None do (because the permutation | ||
| +can be on any other cell set type, which creates an explosion of possible | ||
| +cell types). | ||
| + | ||
| +Like was done with `Threshold` a while ago, this problem is fixed by deep | ||
| +copying the result into a `CellSetExplicit`. This behavior is consistent | ||
| +with VTK. | ||
| diff --git a/vtkm/filter/entity_extraction/testing/UnitTestExtractGeometryFilter.cxx b/vtkm/filter/entity_extraction/testing/UnitTestExtractGeometryFilter.cxx | ||
| index 675df8f77c..14de333666 100644 | ||
| --- a/vtkm/filter/entity_extraction/testing/UnitTestExtractGeometryFilter.cxx | ||
| +++ b/vtkm/filter/entity_extraction/testing/UnitTestExtractGeometryFilter.cxx | ||
| @@ -11,6 +11,7 @@ | ||
| #include <vtkm/cont/testing/MakeTestDataSet.h> | ||
| #include <vtkm/cont/testing/Testing.h> | ||
|
|
||
| +#include <vtkm/filter/clean_grid/CleanGrid.h> | ||
| #include <vtkm/filter/entity_extraction/ExtractGeometry.h> | ||
|
|
||
| using vtkm::cont::testing::MakeTestDataSet; | ||
| @@ -41,11 +42,21 @@ public: | ||
| vtkm::cont::DataSet output = extractGeometry.Execute(dataset); | ||
| VTKM_TEST_ASSERT(test_equal(output.GetNumberOfCells(), 8), "Wrong result for ExtractGeometry"); | ||
|
|
||
| + vtkm::filter::clean_grid::CleanGrid cleanGrid; | ||
| + cleanGrid.SetCompactPointFields(true); | ||
| + cleanGrid.SetMergePoints(false); | ||
| + vtkm::cont::DataSet cleanOutput = cleanGrid.Execute(output); | ||
| + | ||
| vtkm::cont::ArrayHandle<vtkm::Float32> outCellData; | ||
| - output.GetField("cellvar").GetData().AsArrayHandle(outCellData); | ||
| + cleanOutput.GetField("cellvar").GetData().AsArrayHandle(outCellData); | ||
|
|
||
| VTKM_TEST_ASSERT(outCellData.ReadPortal().Get(0) == 21.f, "Wrong cell field data"); | ||
| VTKM_TEST_ASSERT(outCellData.ReadPortal().Get(7) == 42.f, "Wrong cell field data"); | ||
| + | ||
| + vtkm::cont::ArrayHandle<vtkm::Float32> outPointData; | ||
| + cleanOutput.GetField("pointvar").GetData().AsArrayHandle(outPointData); | ||
| + VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(0) == 99); | ||
| + VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(7) == 90); | ||
| } | ||
|
|
||
| static void TestUniformByBox1() | ||
| diff --git a/vtkm/filter/entity_extraction/worklet/ExtractGeometry.h b/vtkm/filter/entity_extraction/worklet/ExtractGeometry.h | ||
| index 97521335f2..449d7eae60 100644 | ||
| --- a/vtkm/filter/entity_extraction/worklet/ExtractGeometry.h | ||
| +++ b/vtkm/filter/entity_extraction/worklet/ExtractGeometry.h | ||
| @@ -10,11 +10,13 @@ | ||
| #ifndef vtkm_m_worklet_ExtractGeometry_h | ||
| #define vtkm_m_worklet_ExtractGeometry_h | ||
|
|
||
| +#include <vtkm/worklet/CellDeepCopy.h> | ||
| #include <vtkm/worklet/WorkletMapTopology.h> | ||
|
|
||
| #include <vtkm/cont/Algorithm.h> | ||
| #include <vtkm/cont/ArrayCopy.h> | ||
| #include <vtkm/cont/ArrayHandle.h> | ||
| +#include <vtkm/cont/CellSetExplicit.h> | ||
| #include <vtkm/cont/CellSetPermutation.h> | ||
| #include <vtkm/cont/CoordinateSystem.h> | ||
| #include <vtkm/cont/Invoker.h> | ||
| @@ -114,28 +116,13 @@ public: | ||
| } | ||
| }; | ||
|
|
||
| - //////////////////////////////////////////////////////////////////////////////////// | ||
| - // Extract cells by ids permutes input data | ||
| - template <typename CellSetType> | ||
| - vtkm::cont::CellSetPermutation<CellSetType> Run(const CellSetType& cellSet, | ||
| - const vtkm::cont::ArrayHandle<vtkm::Id>& cellIds) | ||
| - { | ||
| - using OutputType = vtkm::cont::CellSetPermutation<CellSetType>; | ||
| - | ||
| - vtkm::cont::ArrayCopy(cellIds, this->ValidCellIds); | ||
| - | ||
| - return OutputType(this->ValidCellIds, cellSet); | ||
| - } | ||
| - | ||
| - //////////////////////////////////////////////////////////////////////////////////// | ||
| - // Extract cells by implicit function permutes input data | ||
| template <typename CellSetType, typename ImplicitFunction> | ||
| - vtkm::cont::CellSetPermutation<CellSetType> Run(const CellSetType& cellSet, | ||
| - const vtkm::cont::CoordinateSystem& coordinates, | ||
| - const ImplicitFunction& implicitFunction, | ||
| - bool extractInside, | ||
| - bool extractBoundaryCells, | ||
| - bool extractOnlyBoundaryCells) | ||
| + vtkm::cont::CellSetExplicit<> Run(const CellSetType& cellSet, | ||
| + const vtkm::cont::CoordinateSystem& coordinates, | ||
| + const ImplicitFunction& implicitFunction, | ||
| + bool extractInside, | ||
| + bool extractBoundaryCells, | ||
| + bool extractOnlyBoundaryCells) | ||
| { | ||
| // Worklet output will be a boolean passFlag array | ||
| vtkm::cont::ArrayHandle<bool> passFlags; | ||
| @@ -149,7 +136,10 @@ public: | ||
| vtkm::cont::Algorithm::CopyIf(indices, passFlags, this->ValidCellIds); | ||
|
|
||
| // generate the cellset | ||
| - return vtkm::cont::CellSetPermutation<CellSetType>(this->ValidCellIds, cellSet); | ||
| + vtkm::cont::CellSetPermutation<CellSetType> permutedCellSet(this->ValidCellIds, cellSet); | ||
| + | ||
| + vtkm::cont::CellSetExplicit<> outputCells; | ||
| + return vtkm::worklet::CellDeepCopy::Run(permutedCellSet); | ||
| } | ||
|
|
||
| vtkm::cont::ArrayHandle<vtkm::Id> GetValidCellIds() const { return this->ValidCellIds; } | ||
| -- | ||
| GitLab | ||
|
|
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