ttkRipsComplex.cpp

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#include <ttkMacros.h>
#include <ttkRipsComplex.h>
#include <ttkUtils.h>
 
#include <vtkAbstractArray.h>
#include <vtkCellData.h>
#include <vtkCellType.h>
#include <vtkDoubleArray.h>
#include <vtkInformation.h>
#include <vtkNew.h>
#include <vtkObjectFactory.h>
#include <vtkPointData.h>
#include <vtkTable.h>
#include <vtkType.h>
#include <vtkUnstructuredGrid.h>
 
#include <array>
#include <regex>
 
vtkStandardNewMacro(ttkRipsComplex);
 
ttkRipsComplex::ttkRipsComplex() {
  this->SetNumberOfInputPorts(1);
  this->SetNumberOfOutputPorts(1);
}
 
int ttkRipsComplex::FillInputPortInformation(int port, vtkInformation *info) {
  if(port == 0) {
    info->Set(vtkAlgorithm::INPUT_REQUIRED_DATA_TYPE(), "vtkTable");
    return 1;
  }
  return 0;
}
 
int ttkRipsComplex::FillOutputPortInformation(int port, vtkInformation *info) {
  if(port == 0) {
    info->Set(vtkDataObject::DATA_TYPE_NAME(), "vtkUnstructuredGrid");
    return 1;
  }
  return 0;
}
 
int ttkRipsComplex::RequestData(vtkInformation *ttkNotUsed(request),
                                vtkInformationVector **inputVector,
                                vtkInformationVector *outputVector) {
 
  using ttk::SimplexId;
  ttk::Timer tm{};
 
  auto *input = vtkTable::GetData(inputVector[0]);
  auto *output = vtkUnstructuredGrid::GetData(outputVector);
 
  if(SelectFieldsWithRegexp) {
    // select all input columns whose name is matching the regexp
    ScalarFields.clear();
    const auto n = input->GetNumberOfColumns();
    for(int i = 0; i < n; ++i) {
      const auto &name = input->GetColumnName(i);
      if(std::regex_match(name, std::regex(RegexpString))) {
        ScalarFields.emplace_back(name);
      }
    }
  }
 
  const SimplexId numberOfRows = input->GetNumberOfRows();
  const SimplexId numberOfColumns = ScalarFields.size();
 
  if(numberOfRows <= 0 || numberOfColumns <= 0) {
    this->printErr("Input matrix has invalid dimensions (rows: "
                   + std::to_string(numberOfRows)
                   + ", columns: " + std::to_string(numberOfColumns) + ")");
    return 0;
  }
 
  if(numberOfColumns != numberOfRows) {
    this->printErr("Input distance matrix is not square (rows: "
                   + std::to_string(numberOfRows)
                   + ", columns: " + std::to_string(numberOfColumns) + ")");
    return 0;
  }
 
  std::array<vtkAbstractArray *, 3> components{
    input->GetColumnByName(this->XColumn.data()),
    input->GetColumnByName(this->YColumn.data()),
    input->GetColumnByName(this->ZColumn.data()),
  };
 
  // points from components arrays
  vtkNew<vtkPoints> points{};
  const auto nPoints = components[0]->GetNumberOfTuples();
  points->SetNumberOfPoints(nPoints);
#ifdef TTK_ENABLE_OPENMP
#pragma omp parallel for num_threads(this->threadNumber_)
#endif // TTK_ENABLE_OPENMP
  for(vtkIdType i = 0; i < nPoints; ++i) {
    std::array<float, 3> coords{};
    if(components[0] != nullptr) {
      coords[0] = components[0]->GetVariantValue(i).ToFloat();
    }
    if(components[1] != nullptr && components[1] != components[0]) {
      coords[1] = components[1]->GetVariantValue(i).ToFloat();
    }
    if(components[2] != nullptr && components[2] != components[0]
       && components[2] != components[1]) {
      coords[2] = components[2]->GetVariantValue(i).ToFloat();
    }
    points->SetPoint(i, coords.data());
  }
 
  std::vector<vtkAbstractArray *> arrays{};
  for(const auto &s : ScalarFields) {
    arrays.push_back(input->GetColumnByName(s.data()));
  }
 
  std::vector<std::vector<double>> inputMatrix(numberOfRows);
#ifdef TTK_ENABLE_OPENMP
#pragma omp parallel for num_threads(this->threadNumber_)
#endif // TTK_ENABLE_OPENMP
  for(SimplexId i = 0; i < numberOfRows; ++i) {
    for(size_t j = 0; j < arrays.size(); ++j) {
      inputMatrix[i].emplace_back(arrays[j]->GetVariantValue(i).ToDouble());
    }
  }
 
  std::vector<ttk::SimplexId> vec_connectivity{};
  std::vector<double> diameters{};
  // PointData diameter statistics (min, mean, max)
  vtkNew<vtkDoubleArray> diamMin{}, diamMean{}, diamMax{};
  diamMin->SetName("MinDiameter");
  diamMean->SetName("MeanDiameter");
  diamMax->SetName("MaxDiameter");
  diamMin->SetNumberOfTuples(numberOfRows);
  diamMean->SetNumberOfTuples(numberOfRows);
  diamMax->SetNumberOfTuples(numberOfRows);
  vtkNew<vtkDoubleArray> gaussianDensity{};
  gaussianDensity->SetName("GaussianDensity");
  gaussianDensity->SetNumberOfTuples(numberOfRows);
 
  const auto ret
    = this->execute(vec_connectivity, diameters,
                    std::array<double *const, 3>{
                      ttkUtils::GetPointer<double>(diamMin),
                      ttkUtils::GetPointer<double>(diamMean),
                      ttkUtils::GetPointer<double>(diamMax),
                    },
                    inputMatrix, ttkUtils::GetPointer<double>(gaussianDensity));
 
  if(ret != 0) {
    return 0;
  }
 
  const auto nCells = vec_connectivity.size() / (this->OutputDimension + 1);
  vtkNew<ttkSimplexIdTypeArray> offsets{}, connectivity{};
  offsets->SetNumberOfComponents(1);
  offsets->SetNumberOfTuples(nCells + 1);
  connectivity->SetNumberOfComponents(1);
  connectivity->SetNumberOfTuples(vec_connectivity.size());
 
#ifdef TTK_ENABLE_OPENMP
#pragma omp parallel for num_threads(this->threadNumber_)
#endif // TTK_ENABLE_OPENMP
  for(size_t i = 0; i < nCells + 1; ++i) {
    offsets->SetTuple1(i, i * (this->OutputDimension + 1));
  }
 
#ifdef TTK_ENABLE_OPENMP
#pragma omp parallel for num_threads(this->threadNumber_)
#endif // TTK_ENABLE_OPENMP
  for(size_t i = 0; i < vec_connectivity.size(); ++i) {
    connectivity->SetTuple1(i, vec_connectivity[i]);
  }
 
  // gather arrays to make the UnstructuredGrid
  vtkNew<vtkCellArray> cells{};
#ifndef TTK_ENABLE_64BIT_IDS
  cells->Use32BitStorage();
#endif // TTK_ENABLE_64BIT_IDS
  cells->SetData(offsets, connectivity);
 
  const auto getCellType = [](const SimplexId dim) -> int {
    if(dim == 3) {
      return VTK_TETRA;
    } else if(dim == 2) {
      return VTK_TRIANGLE;
    } else if(dim == 1) {
      return VTK_LINE;
    }
    return VTK_VERTEX;
  };
 
  output->SetPoints(points);
  output->SetCells(getCellType(this->OutputDimension), cells);
 
  // compute cell diameters
  vtkNew<vtkDoubleArray> cellDiameters{};
  cellDiameters->SetNumberOfTuples(nCells);
  cellDiameters->SetName("Diameter");
 
#ifdef TTK_ENABLE_OPENMP
#pragma omp parallel for num_threads(this->threadNumber_)
#endif // TTK_ENABLE_OPENMP
  for(size_t i = 0; i < nCells; ++i) {
    cellDiameters->SetTuple1(i, diameters[i]);
  }
 
  output->GetPointData()->AddArray(diamMin);
  output->GetPointData()->AddArray(diamMean);
  output->GetPointData()->AddArray(diamMax);
  if(this->ComputeGaussianDensity) {
    output->GetPointData()->AddArray(gaussianDensity);
  }
  output->GetCellData()->AddArray(cellDiameters);
 
  if(this->KeepAllDataArrays) {
    auto pd = output->GetPointData();
    if(pd != nullptr) {
      for(vtkIdType i = 0; i < input->GetNumberOfColumns(); ++i) {
        pd->AddArray(input->GetColumn(i));
      }
    }
  }
 
  this->printMsg("Produced " + std::to_string(nCells) + " cells of dimension "
                   + std::to_string(this->OutputDimension),
                 1.0, tm.getElapsedTime(), this->threadNumber_);
 
  return 1;
}