Merge branch 'add-compute-global-point-size' into 'master'

WIP: Add ComputeGlobalPointDimensions

See merge request vtk/vtk-m!2935

examples/contour_tree_distributed/ContourTreeApp.cxx

@@ -155,6 +155,110 @@ private:
   std::vector<std::string> mCLOptions;
 };
 
+void ComputeGlobalPointDimensions(vtkm::cont::PartitionedDataSet& pds)
+{
+  // Compute GlobalPointDimensions as maximum of GlobalPointIndexStart + PointDimensions
+  // for each dimension across all blocks
+
+  // Compute GlobalPointDimensions for all data sets on this MPI rank
+  std::vector<vtkm::Id> globalPointDimensionsThisRank;
+  using ds_const_iterator = vtkm::cont::PartitionedDataSet::const_iterator;
+  for (ds_const_iterator ds_it = pds.cbegin(); ds_it != pds.cend(); ++ds_it)
+  {
+    ds_it->GetCellSet().CastAndCallForTypes<vtkm::cont::CellSetListStructured>(
+      [&globalPointDimensionsThisRank](const auto& css) {
+        globalPointDimensionsThisRank.resize(css.Dimension, -1);
+        for (vtkm::IdComponent d = 0; d < css.Dimension; ++d)
+        {
+          globalPointDimensionsThisRank[d] =
+            std::max(globalPointDimensionsThisRank[d],
+                     css.GetGlobalPointIndexStart()[d] + css.GetPointDimensions()[d]);
+        }
+      });
+  }
+
+  // Perform global reduction to find GlobalPointDimensions across all ranks
+  std::vector<vtkm::Id> globalPointDimensions;
+  auto comm = vtkm::cont::EnvironmentTracker::GetCommunicator();
+  vtkmdiy::mpi::all_reduce(
+    comm, globalPointDimensionsThisRank, globalPointDimensions, vtkmdiy::mpi::maximum<vtkm::Id>{});
+
+  // Set this information in all cell sets
+  using ds_iterator = vtkm::cont::PartitionedDataSet::iterator;
+  for (ds_iterator ds_it = pds.begin(); ds_it != pds.end(); ++ds_it)
+  {
+    // This does not work, i.e., it does not really change the cell set for the DataSet
+    ds_it->GetCellSet().CastAndCallForTypes<vtkm::cont::CellSetListStructured>(
+      [&globalPointDimensions, &ds_it](auto& css) {
+        typename std::remove_reference_t<decltype(css)>::SchedulingRangeType gpd;
+        for (vtkm::IdComponent d = 0; d < css.Dimension; ++d)
+        {
+          gpd[d] = globalPointDimensions[d];
+        }
+        css.SetGlobalPointDimensions(gpd);
+        // Why is the following necessary? Shouldn't it be sufficient to update the
+        // CellSet through the reference?
+        ds_it->SetCellSet(css);
+      });
+  }
+
+  // Debug
+  pds.PrintSummary(std::cout);
+}
+void ShiftLogicalOriginToZero(vtkm::cont::PartitionedDataSet& pds)
+{
+  // Shift the logical origin (minimum of LocalPointIndexStart) to zero
+  // along each dimension
+
+  // Compute minimum global point index start for all data sets on this MPI rank
+  std::vector<vtkm::Id> minimumGlobalPointIndexStartThisRank;
+  using ds_const_iterator = vtkm::cont::PartitionedDataSet::const_iterator;
+  for (ds_const_iterator ds_it = pds.cbegin(); ds_it != pds.cend(); ++ds_it)
+  {
+    ds_it->GetCellSet().CastAndCallForTypes<vtkm::cont::CellSetListStructured>(
+      [&minimumGlobalPointIndexStartThisRank](const auto& css) {
+        minimumGlobalPointIndexStartThisRank.resize(css.Dimension,
+                                                    std::numeric_limits<vtkm::Id>::max());
+        for (vtkm::IdComponent d = 0; d < css.Dimension; ++d)
+        {
+          minimumGlobalPointIndexStartThisRank[d] =
+            std::min(minimumGlobalPointIndexStartThisRank[d], css.GetGlobalPointIndexStart()[d]);
+        }
+      });
+  }
+
+  // Perform global reduction to find GlobalPointDimensions across all ranks
+  std::vector<vtkm::Id> minimumGlobalPointIndexStart;
+  auto comm = vtkm::cont::EnvironmentTracker::GetCommunicator();
+  vtkmdiy::mpi::all_reduce(comm,
+                           minimumGlobalPointIndexStartThisRank,
+                           minimumGlobalPointIndexStart,
+                           vtkmdiy::mpi::minimum<vtkm::Id>{});
+
+  // Shift all cell sets so that minimum global point index start
+  // along each dimension is zero
+  using ds_iterator = vtkm::cont::PartitionedDataSet::iterator;
+  for (ds_iterator ds_it = pds.begin(); ds_it != pds.end(); ++ds_it)
+  {
+    // This does not work, i.e., it does not really change the cell set for the DataSet
+    ds_it->GetCellSet().CastAndCallForTypes<vtkm::cont::CellSetListStructured>(
+      [&minimumGlobalPointIndexStart, &ds_it](auto& css) {
+        auto pointIndexStart = css.GetGlobalPointIndexStart();
+        typename std::remove_reference_t<decltype(css)>::SchedulingRangeType shiftedPointIndexStart;
+        for (vtkm::IdComponent d = 0; d < css.Dimension; ++d)
+        {
+          shiftedPointIndexStart[d] = pointIndexStart[d] - minimumGlobalPointIndexStart[d];
+        }
+        css.SetGlobalPointIndexStart(shiftedPointIndexStart);
+        // Why is the following necessary? Shouldn't it be sufficient to update the
+        // CellSet through the reference?
+        ds_it->SetCellSet(css);
+      });
+  }
+
+  // Debug
+  //pds.PrintSummary(std::cout);
+}
 
 // Compute and render an isosurface for a uniform grid example
 int main(int argc, char* argv[])
@@ -652,6 +756,8 @@ int main(int argc, char* argv[])
   filter.SetActiveField("values");
 
   // Execute the contour tree analysis
+  ShiftLogicalOriginToZero(useDataSet);
+  ComputeGlobalPointDimensions(useDataSet);
   auto result = filter.Execute(useDataSet);
 
   currTime = totalTime.GetElapsedTime();

examples/contour_tree_distributed/ContourTreeAppDataIO.h

@@ -346,7 +346,8 @@ bool read3DHDF5File(const int& mpi_rank,
   ds = dsb.Create(v_dims, v_origin, v_spacing);
   vtkm::cont::CellSetStructured<3> cs;
   cs.SetPointDimensions(v_dims);
-  cs.SetGlobalPointDimensions(globalSize);
+  // NOTE: Comment out for test purposes
+  //cs.SetGlobalPointDimensions(globalSize);
   cs.SetGlobalPointIndexStart(vtkm::Id3{ v_origin[0], v_origin[1], v_origin[2] });
   ds.SetCellSet(cs);
 
@@ -587,7 +588,8 @@ bool readPreSplitFiles(const int& rank,
       ds = dsb.Create(v_dims, v_origin, v_spacing);
       vtkm::cont::CellSetStructured<2> cs;
       cs.SetPointDimensions(v_dims);
-      cs.SetGlobalPointDimensions(vtkm::Id2{ globalSize[0], globalSize[1] });
+      // NOTE: Comment out for test purposes
+      //cs.SetGlobalPointDimensions(vtkm::Id2{ globalSize[0], globalSize[1] });
       cs.SetGlobalPointIndexStart(vtkm::Id2{ offset[0], offset[1] });
       ds.SetCellSet(cs);
     }
@@ -604,7 +606,8 @@ bool readPreSplitFiles(const int& rank,
       ds = dsb.Create(v_dims, v_origin, v_spacing);
       vtkm::cont::CellSetStructured<3> cs;
       cs.SetPointDimensions(v_dims);
-      cs.SetGlobalPointDimensions(globalSize);
+      // NOTE: Comment out for test purposes
+      //cs.SetGlobalPointDimensions(globalSize);
       cs.SetGlobalPointIndexStart(vtkm::Id3{ offset[0], offset[1], offset[2] });
       ds.SetCellSet(cs);
     }
@@ -815,7 +818,8 @@ bool readSingleBlockFile(const int& rank,
         ds = dsb.Create(vdims, origin, spacing);
         vtkm::cont::CellSetStructured<2> cs;
         cs.SetPointDimensions(vdims);
-        cs.SetGlobalPointDimensions(vtkm::Id2{ globalSize[0], globalSize[1] });
+        // NOTE: Comment out for test purposes
+        //cs.SetGlobalPointDimensions(vtkm::Id2{ globalSize[0], globalSize[1] });
         cs.SetGlobalPointIndexStart(vtkm::Id2{ 0, (blockStart / blockSliceSize) });
         ds.SetCellSet(cs);
         localBlockIndicesPortal.Set(localBlockIndex, vtkm::Id3(0, blockIndex, 0));
@@ -832,7 +836,8 @@ bool readSingleBlockFile(const int& rank,
         ds = dsb.Create(vdims, origin, spacing);
         vtkm::cont::CellSetStructured<3> cs;
         cs.SetPointDimensions(vdims);
-        cs.SetGlobalPointDimensions(globalSize);
+        // NOTE: Comment out for test purposes
+        //cs.SetGlobalPointDimensions(globalSize);
         cs.SetGlobalPointIndexStart(vtkm::Id3(0, 0, blockStart / blockSliceSize));
         ds.SetCellSet(cs);
         localBlockIndicesPortal.Set(localBlockIndex, vtkm::Id3(0, 0, blockIndex));

vtkm/cont/testlib/MakeTestDataSet.cxx

@@ -233,33 +233,56 @@ vtkm::cont::DataSet MakeTestDataSet::Make3DUniformDataSet1()
   constexpr vtkm::Id nVerts = 125;
   constexpr vtkm::Id nCells = 64;
   constexpr vtkm::Float32 pointvar[nVerts] = {
-    0.0f,  0.0f, 0.0f, 0.0f,  0.0f,  0.0f,  0.0f,  0.0f,  0.0f,  0.0f, 0.0f, 0.0f,  0.0f,
-    0.0f,  0.0f, 0.0f, 0.0f,  0.0f,  0.0f,  0.0f,  0.0f,  0.0f,  0.0f, 0.0f, 0.0f,
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 0, 0
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 1, 0
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 2, 0
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 3, 0
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 4, 0
 
-    0.0f,  0.0f, 0.0f, 0.0f,  0.0f,  0.0f,  99.0f, 90.0f, 85.0f, 0.0f, 0.0f, 95.0f, 80.0f,
-    95.0f, 0.0f, 0.0f, 85.0f, 90.0f, 99.0f, 0.0f,  0.0f,  0.0f,  0.0f, 0.0f, 0.0f,
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 0, 1
+    0.0f, 99.0f, 90.0f, 85.0f, 0.0f, // 0-4, 1, 1
+    0.0f, 95.0f, 80.0f, 95.0f, 0.0f, // 0-4, 2, 1
+    0.0f, 85.0f, 90.0f, 99.0f, 0.0f, // 0-4, 3, 1
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 4, 1
 
-    0.0f,  0.0f, 0.0f, 0.0f,  0.0f,  0.0f,  75.0f, 50.0f, 65.0f, 0.0f, 0.0f, 55.0f, 15.0f,
-    45.0f, 0.0f, 0.0f, 60.0f, 40.0f, 70.0f, 0.0f,  0.0f,  0.0f,  0.0f, 0.0f, 0.0f,
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 0, 2
+    0.0f, 75.0f, 50.0f, 65.0f, 0.0f, // 0-4, 1, 2
+    0.0f, 55.0f, 15.0f, 45.0f, 0.0f, // 0-4, 2, 2
+    0.0f, 60.0f, 40.0f, 70.0f, 0.0f, // 0-4, 3, 2
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 4, 2
 
-    0.0f,  0.0f, 0.0f, 0.0f,  0.0f,  0.0f,  97.0f, 87.0f, 82.0f, 0.0f, 0.0f, 92.0f, 77.0f,
-    92.0f, 0.0f, 0.0f, 82.0f, 87.0f, 97.0f, 0.0f,  0.0f,  0.0f,  0.0f, 0.0f, 0.0f,
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 0, 3
+    0.0f, 97.0f, 87.0f, 82.0f, 0.0f, // 0-4, 1, 3
+    0.0f, 92.0f, 77.0f, 92.0f, 0.0f, // 0-4, 2, 3
+    0.0f, 82.0f, 87.0f, 97.0f, 0.0f, // 0-4, 3, 3
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 4, 3
 
-    0.0f,  0.0f, 0.0f, 0.0f,  0.0f,  0.0f,  0.0f,  0.0f,  0.0f,  0.0f, 0.0f, 0.0f,  0.0f,
-    0.0f,  0.0f, 0.0f, 0.0f,  0.0f,  0.0f,  0.0f,  0.0f,  0.0f,  0.0f, 0.0f, 0.0f
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 0, 4
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 1, 4
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 2, 4
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f, // 0-4, 3, 4
+    0.0f, 0.0f,  0.0f,  0.0f,  0.0f  // 0-4, 4, 4
   };
   constexpr vtkm::Float32 cellvar[nCells] = {
-    0.0f,  1.0f,  2.0f,  3.0f,  4.0f,  5.0f,  6.0f,  7.0f,
-    8.0f,  9.0f,  10.0f, 11.0f, 12.0f, 13.0f, 14.0f, 15.0f,
+    0.0f,  1.0f,  2.0f,  3.0f,  // 0-3, 0, 0
+    4.0f,  5.0f,  6.0f,  7.0f,  // 0-3, 1, 0
+    8.0f,  9.0f,  10.0f, 11.0f, // 0-3, 2, 0
+    12.0f, 13.0f, 14.0f, 15.0f, // 0-3, 3, 0
 
-    16.0f, 17.0f, 18.0f, 19.0f, 20.0f, 21.0f, 22.0f, 23.0f,
-    24.0f, 25.0f, 26.0f, 27.0f, 28.0f, 29.0f, 30.0f, 31.0f,
+    16.0f, 17.0f, 18.0f, 19.0f, // 0-3, 0, 1
+    20.0f, 21.0f, 22.0f, 23.0f, // 0-3, 1, 1
+    24.0f, 25.0f, 26.0f, 27.0f, // 0-3, 2, 1
+    28.0f, 29.0f, 30.0f, 31.0f, // 0-3, 3, 1
 
-    32.0f, 33.0f, 34.0f, 35.0f, 36.0f, 37.0f, 38.0f, 39.0f,
-    40.0f, 41.0f, 42.0f, 43.0f, 44.0f, 45.0f, 46.0f, 47.0f,
+    32.0f, 33.0f, 34.0f, 35.0f, // 0-3, 0, 2
+    36.0f, 37.0f, 38.0f, 39.0f, // 0-3, 1, 2
+    40.0f, 41.0f, 42.0f, 43.0f, // 0-3, 2, 2
+    44.0f, 45.0f, 46.0f, 47.0f, // 0-3, 3, 2
 
-    48.0f, 49.0f, 50.0f, 51.0f, 52.0f, 53.0f, 54.0f, 55.0f,
-    56.0f, 57.0f, 58.0f, 59.0f, 60.0f, 61.0f, 62.0f, 63.0f
+    48.0f, 49.0f, 50.0f, 51.0f, // 0-3, 0, 3
+    52.0f, 53.0f, 54.0f, 55.0f, // 0-3, 1, 3
+    56.0f, 57.0f, 58.0f, 59.0f, // 0-3, 2, 3
+    60.0f, 61.0f, 62.0f, 63.0f  // 0-3, 3, 3
   };
 
   dataSet.AddPointField("pointvar", pointvar, nVerts);

vtkm/filter/entity_extraction/ExtractStructured.h

@@ -85,17 +85,23 @@ public:
   VTKM_CONT
   void SetSampleRate(vtkm::Id3 sampleRate) { this->SampleRate = sampleRate; }
 
-  // Get if we should include the outer boundary on a subsample
-  // (NOTE: This method is deprecated because it is not clear from either
-  // the documentation or the source code what the intention of this feature
-  // is. If your are using this method somewhere and think it should remain,
-  // please open a merge request to "de-deprecate" it and add a test and
-  // documentation of the expected behavior.)
-  VTKM_DEPRECATED(2.2)
+  /// @brief Specifies if the outer boundary should always be included.
+  ///
+  /// When a subsample rate is specified, it is possible that some of the
+  /// boundary samples will not be included in the sampling. If this is the
+  /// case and `IncludeBoundary` is set to true, then an extra sample is
+  /// set in the output and the values on the boundary are included. For example,
+  /// say the input has resolution (5, 5, 1) (and the VOI matches), and the sample
+  /// rate is set to (3, 3, 1). If `IncludeBoundary` is false, then the output will
+  /// have the 4 points that correspond to the 3D indices (0, 0, 0), (3, 0, 0),
+  /// (0, 3, 0), and (3, 3, 0) of the input. This misses the outer boundary at
+  /// index 4 in the x and y directions. If `IncludeBoundary is set to true, then
+  /// the output will have the 9 points that correspond to the 3D indices (0, 0, 0),
+  /// (3, 0, 0), (4, 0, 0), (0, 3, 0), (3, 3, 0), (4, 3, 0), (0, 4, 0), (3, 4, 0),
+  /// and (4, 4, 0) to capture this outer boundary.
   VTKM_CONT
   bool GetIncludeBoundary() const { return this->IncludeBoundary; }
-  // Set if we should include the outer boundary on a subsample
-  VTKM_DEPRECATED(2.2)
+  /// @copydoc GetIncludeBoundary
   VTKM_CONT
   void SetIncludeBoundary(bool value) { this->IncludeBoundary = value; }
 

vtkm/filter/entity_extraction/testing/UnitTestExtractStructuredFilter.cxx

@@ -341,7 +341,7 @@ public:
 
   static void TestUniform3D7()
   {
-    std::cout << "Testing extract structured uniform" << std::endl;
+    std::cout << "Testing extract structured uniform, exclude boundary" << std::endl;
     vtkm::cont::DataSet dataset = MakeTestDataSet().Make3DUniformDataSet1();
 
     vtkm::filter::entity_extraction::ExtractStructured extract;
@@ -351,6 +351,7 @@ public:
     vtkm::Id3 sample(3, 3, 2);
     extract.SetVOI(range);
     extract.SetSampleRate(sample);
+    extract.SetIncludeBoundary(false); // default
 
     extract.SetFieldsToPass({ "pointvar", "cellvar" });
     vtkm::cont::DataSet output = extract.Execute(dataset);
@@ -371,16 +372,16 @@ public:
                      "Data/Geometry mismatch for ExtractStructured filter");
 
     VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(0) == 0.0f, "Wrong point field data");
+    VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(3) == 99.0f, "Wrong point field data");
+    VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(4) == 0.0f, "Wrong point field data");
     VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(7) == 97.0f, "Wrong point field data");
 
     VTKM_TEST_ASSERT(outCellData.ReadPortal().Get(0) == 16.0f, "Wrong cell field data");
   }
 
-  VTKM_DEPRECATED_SUPPRESS_BEGIN
-  // This test repeates TestUniform3D7 but uses deprecated behavior.
   static void TestUniform3D8()
   {
-    std::cout << "Testing extract structured uniform" << std::endl;
+    std::cout << "Testing extract structured uniform, include boundary" << std::endl;
     vtkm::cont::DataSet dataset = MakeTestDataSet().Make3DUniformDataSet1();
     vtkm::filter::entity_extraction::ExtractStructured extract;
 
@@ -411,12 +412,15 @@ public:
 
     VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(0) == 0.0f, "Wrong point field data");
     VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(4) == 99.0f, "Wrong point field data");
+    VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(5) == 0.0f, "Wrong point field data");
+    VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(7) == 0.0f, "Wrong point field data");
     VTKM_TEST_ASSERT(outPointData.ReadPortal().Get(13) == 97.0f, "Wrong point field data");
 
     VTKM_TEST_ASSERT(outCellData.ReadPortal().Get(0) == 16.0f, "Wrong cell field data");
+    VTKM_TEST_ASSERT(outCellData.ReadPortal().Get(1) == 19.0f, "Wrong cell field data");
+    VTKM_TEST_ASSERT(outCellData.ReadPortal().Get(2) == 28.0f, "Wrong cell field data");
     VTKM_TEST_ASSERT(outCellData.ReadPortal().Get(3) == 31.0f, "Wrong cell field data");
   }
-  VTKM_DEPRECATED_SUPPRESS_END
 
   static void TestRectilinear2D()
   {