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/* Copyright (c) 2008-2022 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "as is"
* basis, without warranty of any kind, either expressed, implied, or
* statutory, including, without limitation, warranties that the
* Covered Software is free of defects, merchantable, fit for a
* particular purpose or non-infringing.
* See the Mozilla Public License v. 2.0 for more details.
*
* For more details, see http://www.mrtrix.org/.
*/
#ifndef __interp_base_h__
#define __interp_base_h__
#include "image_helpers.h"
#include "transform.h"
namespace MR
{
class Header;
namespace Interp
{
//! \addtogroup interp
// @{
//! This class defines the interface for classes that perform image interpolation
/*! Interpolation is generally performed along the first 3 (spatial) axes;
* the (integer) position along the remaining axes should be set using the
* template ImageType class.
* The spatial coordinates can be set using the functions voxel(), image(),
* and scanner().
* For example:
* \code
* auto input = Image<float>::create (argument[0]);
*
* // create an Interp::Cubic object using input as the parent data set:
* Interp::Cubic<decltype(input)> interp (input);
*
* // set the scanner-space position to [ 10.2 3.59 54.1 ]:
* interp.scanner (10.2, 3.59, 54.1);
*
* // get the value at this position:
* float value = interp.value();
* \endcode
*
* The template \a input class must be usable with this type of syntax:
* \code
* int xsize = input.size(0); // return the dimension
* int ysize = input.size(1); // along the x, y & z dimensions
* int zsize = input.size(2);
* float v[] = { input.spacing(0), input.spacing(1), input.spacing(2) }; // return voxel dimensions
* input.index(0) = 0; // these lines are used to
* input.index(1)--; // set the current position
* input.index(2)++; // within the data set
* float f = input.value();
* transform_type M = input.transform(); // a valid 4x4 transformation matrix
* \endcode
*/
template <class ImageType> class Base : public ImageType, public Transform
{ MEMALIGN(Base<ImageType>)
public:
using image_type = ImageType;
using value_type = typename ImageType::value_type;
//! construct an Interp object to obtain interpolated values using the
//! parent ImageType class
Base (const ImageType& parent, value_type value_when_out_of_bounds = default_out_of_bounds_value()) :
ImageType (parent),
Transform (parent),
out_of_bounds_value (value_when_out_of_bounds),
bounds { parent.size(0) - 0.5, parent.size(1) - 0.5, parent.size(2) - 0.5 },
out_of_bounds (true) { }
//! Functions that must be defined by interpolation classes
/*! The follwing functions must be defined by any derived
* interpolation class. They are NOT defined as virtual functions
* here in order to prevent use of vtables in performance-critical
* code; nevertheless, the interface should be consistent for all
* derived interpolation classes. */
//! Set the current position to <b>voxel space</b> position \a pos
/*! This will set the position from which the image intensity values will
* be interpolated, assuming that \a pos provides the position as a
* (floating-point) voxel coordinate within the dataset.
* Interpolation classes need to provide a specialization of this method.
* Note that unlike some previous code versions, a TRUE return value
* indicates that the point is WITHIN the image volume.
*
* \code
* template <class VectorType> bool voxel (const VectorType& pos);
* \endcode
* */
//! Set the current position to <b>image space</b> position \a pos
/*! This will set the position from which the image intensity values will
* be interpolated, assuming that \a pos provides the position as a
* coordinate relative to the axes of the dataset, in units of
* millimeters. The origin is taken to be the centre of the voxel at [
* 0 0 0 ].
*
* Derived classes should reproduce the code exactly as it appears below:
*
* \code
* template <class VectorType>
* FORCE_INLINE bool image (const VectorType& pos) {
* return voxel (Transform::voxelsize.inverse() * pos.template cast<default_type>());
* }
* \endcode
*/
//! Set the current position to the <b>scanner space</b> position \a pos
/*! This will set the position from which the image intensity values will
* be interpolated, assuming that \a pos provides the position as a
* scanner space coordinate, in units of millimeters.
*
* Derived classes should reproduce the code exactly as it appears below:
*
* \code
* template <class VectorType>
* FORCE_INLINE bool scanner (const VectorType& pos) {
* return voxel (Transform::scanner2voxel * pos.template cast<default_type>());
* }
* \endcode
*/
//! Read an interpolated value from the current position
/*! This function must be preceded by a call to voxel(), image() or
* scanner(), and perform the core functionality of the derived
* interpolator class - that is, generating an intensity value
* based on the image data. The precise implementation of this
* function will therefore depend on the nature of the interpolator.
*
* \code
* FORCE_INLINE value_type value ()
* {
if (out_of_bounds)
return out_of_bounds_value;
{ ... }
* }
* \endcode
* */
//! Read interpolated values from volumes along axis >= 3
/*! This function uses the initialisation of interpolation position
* from the voxel(), image() or scanner() functions to produce
* interpolated values across a set of volumes, making the
* process of interpolation much faster. The specific implementation
* of this function, and indeed whether or not the initialisation
* from the voxel() function can be exploited across multiple
* volumes, will depend on the specific details of the interpolator.
*
* \code
* Eigen::Matrix<value_type, Eigen::Dynamic, 1> row (size_t axis)
* {
* assert (axis > 2);
* assert (axis < ImageType::ndim());
* if (out_of_bounds) {
* Eigen::Matrix<value_type, Eigen::Dynamic, 1> out_of_bounds_row (ImageType::size(axis));
* out_of_bounds_row.setOnes();
* out_of_bounds_row *= out_of_bounds_value;
* return out_of_bounds_row;
* }
* { ... }
* }
* \endcode
* */
// Value to return when the position is outside the bounds of the image volume
const value_type out_of_bounds_value;
static inline value_type default_out_of_bounds_value () {
return std::numeric_limits<value_type>::quiet_NaN();
}
//! test whether current position is within bounds.
/*! \return true if the current position is out of bounds, false otherwise */
bool operator! () const { return out_of_bounds; }
protected:
default_type bounds[3];
bool out_of_bounds;
// Some helper functions
template <class VectorType>
bool set_out_of_bounds (const VectorType& pos) {
return ((out_of_bounds = (pos[0] <= -0.5 || pos[0] >= bounds[0] ||
pos[1] <= -0.5 || pos[1] >= bounds[1] ||
pos[2] <= -0.5 || pos[2] >= bounds[2])));
}
void set_out_of_bounds (const bool value) {
out_of_bounds = value;
}
template <class VectorType>
Eigen::Vector3d intravoxel_offset (const VectorType& pos) {
if (set_out_of_bounds (pos))
return Eigen::Vector3d (NaN, NaN, NaN);
return Eigen::Vector3d (pos[0]-std::floor (pos[0]), pos[1]-std::floor (pos[1]), pos[2]-std::floor (pos[2]));
}
};
//! @}
}
}
#endif
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