add H5part reader

Moving H5part reader from ParaView over to VTK.

IO/H5part/CMakeLists.txt

+set(classes
+  vtkH5PartReader)
+
+vtk_module_add_module(VTK::IOH5part
+  CLASSES ${classes})
+
+vtk_module_definitions(VTK::IOH5part
+  PRIVATE
+    H5_USE_16_API)

IO/H5part/Testing/CMakeLists.txt

+vtk_module_test_data(
+  Data/H5part/sample.h5part)
+
+add_subdirectory(Cxx)

IO/H5part/Testing/Cxx/CMakeLists.txt

+vtk_add_test_cxx(vtkIOH5partCxxTests tests
+  TestH5partReader.cxx,NO_VALID
+)
+vtk_test_cxx_executable(vtkIOH5partCxxTests tests)

IO/H5part/Testing/Cxx/TestH5partReader.cxx

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    TestH5partReader.cxx
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+#include "vtkH5PartReader.h"
+#include "vtkNew.h"
+#include "vtkPointData.h"
+#include "vtkPolyData.h"
+#include "vtkTestUtilities.h"
+
+int TestH5partReader(int argc, char* argv[])
+{
+  char* fname = vtkTestUtilities::ExpandDataFileName(argc, argv, "Data/H5part/sample.h5part");
+  vtkNew<vtkH5PartReader> reader;
+  reader->SetFileName(fname);
+  delete[] fname;
+
+  reader->UpdateInformation();
+
+  if (strcmp(reader->GetXarray(), "x") != 0 || strcmp(reader->GetYarray(), "y") != 0 ||
+    strcmp(reader->GetZarray(), "z") != 0)
+  {
+    cerr << "ERROR: incorrect arrays chosen by default!" << endl;
+    return EXIT_FAILURE;
+  }
+
+  reader->EnableAll();
+  reader->Update();
+
+  auto output = reader->GetOutput();
+  if (output->GetNumberOfPoints() != 1000)
+  {
+    cerr << "ERROR: mismatched point count" << endl;
+    return EXIT_FAILURE;
+  }
+
+  if (output->GetPointData()->GetNumberOfArrays() != 7)
+  {
+    cerr << "ERROR: mismatched array count" << endl;
+    return EXIT_FAILURE;
+  }
+
+  return EXIT_SUCCESS;
+}

IO/H5part/vtk.module

+NAME
+  VTK::IOH5part
+LIBRARY_NAME
+  vtkIOH5part
+KIT
+  VTK::IO
+DEPENDS
+  VTK::CommonCore
+  VTK::CommonDataModel
+  VTK::CommonExecutionModel
+PRIVATE_DEPENDS
+  VTK::h5part
+  VTK::hdf5
+  VTK::vtksys
+TEST_DEPENDS
+  VTK::TestingRendering

IO/H5part/vtkH5PartReader.h

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    vtkH5PartReader.h
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+/*=========================================================================
+
+  Copyright (C) CSCS - Swiss National Supercomputing Centre.
+  You may use modify and and distribute this code freely providing
+  1) This copyright notice appears on all copies of source code
+  2) An acknowledgment appears with any substantial usage of the code
+  3) If this code is contributed to any other open source project, it
+  must not be reformatted such that the indentation, bracketing or
+  overall style is modified significantly.
+
+  This software is distributed WITHOUT ANY WARRANTY; without even the
+  implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+=========================================================================*/
+/**
+ * @class vtkH5PartReader
+ * @brief Read H5Part particle files
+ *
+ * vtkH5PartReader reads compatible with H5Part : documented here
+ * http://amas.web.psi.ch/docs/H5Part-doc/h5part.html
+ *
+ * @note Thanks to John Bidiscombe of
+ * CSCS - Swiss National Supercomputing Centre for creating and contributing
+ * the original implementation of this class.
+ */
+
+#ifndef vtkH5PartReader_h
+#define vtkH5PartReader_h
+
+#include "vtkIOH5partModule.h" // for export macro
+#include "vtkPolyDataAlgorithm.h"
+
+#include <string> // for string
+#include <vector> // for vector
+
+class vtkDataArraySelection;
+struct H5PartFile;
+class VTKIOH5PART_EXPORT vtkH5PartReader : public vtkPolyDataAlgorithm
+{
+public:
+  static vtkH5PartReader* New();
+  vtkTypeMacro(vtkH5PartReader, vtkPolyDataAlgorithm);
+  void PrintSelf(ostream& os, vtkIndent indent) override;
+
+  //@{
+  /**
+   * Specify file name.
+   */
+  void SetFileName(char* filename);
+  vtkGetStringMacro(FileName);
+  //@}
+
+  //@{
+  /**
+   * Set/Get the array that will be used for the X coordinates
+   */
+  vtkGetStringMacro(Xarray);
+  vtkSetStringMacro(Xarray);
+  //@}
+
+  //@{
+  /**
+   * Set/Get the array that will be used for the Y coordinates
+   */
+  vtkGetStringMacro(Yarray);
+  vtkSetStringMacro(Yarray);
+  //@}
+
+  //@{
+  /**
+   * Set/Get the array that will be used for the Z coordinates
+   */
+  vtkGetStringMacro(Zarray);
+  vtkSetStringMacro(Zarray);
+  //@}
+
+  //@{
+  /**
+   * When set (default no), the reader will generate a vertex cell
+   * for each point/particle read. When using the points directly
+   * this is unnecessary and time can be saved by omitting cell generation
+   * vtkPointSpriteMapper does not require them.
+   * When using ParaView, cell generation is recommended, without them
+   * many filter operations are unavailable
+   */
+  vtkSetMacro(GenerateVertexCells, int);
+  vtkGetMacro(GenerateVertexCells, int);
+  vtkBooleanMacro(GenerateVertexCells, int);
+  //@}
+
+  //@{
+  /**
+  * When this option is set, scalar fields with names which form a pattern
+  * of the form scalar_0, scalar_1, scalar_2 will be combined into a single
+  * vector field with N components
+  */
+  vtkSetMacro(CombineVectorComponents, int);
+  vtkGetMacro(CombineVectorComponents, int);
+  vtkBooleanMacro(CombineVectorComponents, int);
+  //@}
+
+  //@{
+  /**
+  * Normally, a request for data at time t=x, where x is either before the start of
+  * time for the data, or after the end, will result in the first or last
+  * timestep of data to be retrieved (time is clamped to max/min values).
+  * Forsome applications/animations, it may be desirable to not display data
+  * for invalid times. When MaskOutOfTimeRangeOutput is set to ON, the reader
+  * will return an empty dataset for out of range requests. This helps
+  * avoid corruption of animations.
+  */
+  vtkSetMacro(MaskOutOfTimeRangeOutput, int);
+  vtkGetMacro(MaskOutOfTimeRangeOutput, int);
+  vtkBooleanMacro(MaskOutOfTimeRangeOutput, int);
+  //@}
+
+  //@{
+  /**
+  * An H5Part file may contain multiple arrays
+  * a GUI (eg Paraview) can provide a mechanism for selecting which data arrays
+  * are to be read from the file. The PointArray variables and members can
+  * be used to query the names and number of arrays available
+  * and set the status (on/off) for each array, thereby controlling which
+  * should be read from the file. Paraview queries these point arrays after
+  * the (update) information part of the pipeline has been updated, and before the
+  * (update) data part is updated.
+  */
+  int GetNumberOfPointArrays();
+  const char* GetPointArrayName(int index);
+  int GetPointArrayStatus(const char* name);
+  void SetPointArrayStatus(const char* name, int status);
+  void DisableAll();
+  void EnableAll();
+  void Disable(const char* name);
+  void Enable(const char* name);
+
+  int GetNumberOfPointArrayStatusArrays() { return GetNumberOfPointArrays(); }
+  const char* GetPointArrayStatusArrayName(int index) { return GetPointArrayName(index); }
+  int GetPointArrayStatusArrayStatus(const char* name) { return GetPointArrayStatus(name); }
+  void SetPointArrayStatusArrayStatus(const char* name, int status)
+  {
+    this->SetPointArrayStatus(name, status);
+  }
+
+  //@}
+
+  //@{
+  int GetNumberOfCoordinateArrays() { return GetNumberOfPointArrays(); }
+  const char* GetCoordinateArrayName(int index) { return GetPointArrayName(index); }
+  int GetCoordinateArrayStatus(const char* name);
+  void SetCoordinateArrayStatus(const char* name, int status);
+  //@}
+
+protected:
+  vtkH5PartReader();
+  ~vtkH5PartReader() override;
+  //
+  int RequestInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) override;
+  int RequestData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) override;
+  int OpenFile();
+  void CloseFile();
+  //  void  CopyIntoCoords(int offset, vtkDataArray *source, vtkDataArray *dest);
+  // returns 0 if no, returns 1,2,3,45 etc for the first, second...
+  // example : if CombineVectorComponents is true, then
+  // velocity_0 returns 1, velocity_1 returns 2 etc
+  // if CombineVectorComponents is false, then
+  // velocity_0 returns 0, velocity_1 returns 0 etc
+  int IndexOfVectorComponent(const char* name);
+
+  std::string NameOfVectorComponent(const char* name);
+
+  //
+  // Internal Variables
+  //
+  char* FileName;
+  int NumberOfTimeSteps;
+  int TimeStep;
+  int ActualTimeStep;
+  double TimeStepTolerance;
+  int CombineVectorComponents;
+  int GenerateVertexCells;
+  H5PartFile* H5FileId;
+  vtkTimeStamp FileModifiedTime;
+  vtkTimeStamp FileOpenedTime;
+  int MaskOutOfTimeRangeOutput;
+  int TimeOutOfRange;
+  //
+  char* Xarray;
+  char* Yarray;
+  char* Zarray;
+
+  std::vector<double> TimeStepValues;
+
+  // To allow paraview gui to enable/disable scalar reading
+  vtkDataArraySelection* PointDataArraySelection;
+
+private:
+  vtkH5PartReader(const vtkH5PartReader&) = delete;
+  void operator=(const vtkH5PartReader&) = delete;
+};
+
+#endif

Testing/Data/H5part/sample.h5part.sha512

+bea4e3debb16b8a2abee15ecba6997c6b1ef626db4e84cc6191d37154e0b352d3074b8e5d133ce3b82ac06eb4019adfb43db0a732f7f70a523fd81e726992d91