ContinuousMeasures.h

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#ifndef INCLUDE_MOLASSEMBLER_SHAPES_CONTINUOUS_MEASURES_H
#define INCLUDE_MOLASSEMBLER_SHAPES_CONTINUOUS_MEASURES_H

#include "Molassembler/Shapes/PointGroupElements.h"
#include "Molassembler/Shapes/Data.h"

namespace Scine {
namespace Molassembler {
namespace Shapes {

namespace Continuous {

using PositionCollection = Eigen::Matrix<double, 3, Eigen::Dynamic>;

MASM_EXPORT PositionCollection normalize(const PositionCollection& positions);

namespace Fixed {

MASM_EXPORT double element(
  const PositionCollection& normalizedPositions,
  const Elements::Rotation& rotation
);

MASM_EXPORT double element(
  const PositionCollection& normalizedPositions,
  const Elements::Reflection& reflection
);

MASM_EXPORT double Cinf(
  const PositionCollection& normalizedPositions,
  const Eigen::Vector3d& axis
);

} // namespace Fixed

MASM_EXPORT std::pair<double, Elements::Rotation> element(
  const PositionCollection& normalizedPositions,
  Elements::Rotation rotation
);

MASM_EXPORT std::pair<double, Elements::Reflection> element(
  const PositionCollection& normalizedPositions,
  Elements::Reflection reflection
);

MASM_EXPORT double element(
  const PositionCollection& normalizedPositions,
  const Elements::Inversion& /* inversion */
);

MASM_EXPORT double Cinf(const PositionCollection& normalizedPositions);

MASM_EXPORT double pointGroup(
  const PositionCollection& normalizedPositions,
  PointGroup pointGroup
);

struct MASM_EXPORT ShapeResult {
  std::vector<Vertex> mapping;
  double measure;
};

MASM_EXPORT ShapeResult shapeFaithfulPaperImplementation(
  const PositionCollection& normalizedPositions,
  Shape shape
);

MASM_EXPORT ShapeResult shapeAlternateImplementation(
  const PositionCollection& normalizedPositions,
  Shape shape
);

MASM_EXPORT ShapeResult shapeAlternateImplementationCentroidLast(
  const PositionCollection& normalizedPositions,
  Shape shape
);

MASM_EXPORT ShapeResult shapeHeuristics(
  const PositionCollection& normalizedPositions,
  Shape shape
);

MASM_EXPORT ShapeResult shapeHeuristicsCentroidLast(
  const PositionCollection& normalizedPositions,
  Shape shape
);

MASM_EXPORT ShapeResult shape(
  const PositionCollection& normalizedPositions,
  Shape shape
);

MASM_EXPORT ShapeResult shapeCentroidLast(
  const PositionCollection& normalizedPositions,
  const Shape shape
);

MASM_EXPORT double minimumDistortionAngle(Shape a, Shape b);

MASM_EXPORT double minimalDistortionPathDeviation(
  const PositionCollection& positions,
  Shape a,
  Shape b,
  const double minimumDistortionAngle
);

MASM_EXPORT double minimalDistortionPathDeviation(const PositionCollection& positions, Shape a, Shape b);

MASM_EXPORT std::array<double, 4> randomCloudDistributionParameters(
  Shape shape,
  unsigned N,
  unsigned seed
);

MASM_EXPORT boost::optional<double> probabilityRandomCloud(double measure, Shape shape);

} // namespace Continuous
} // namespace Shapes
} // namespace Molassembler
} // namespace Scine

#endif