/usr/include/mia-2.2/mia/2d/transform.hh is in libmia-2.2-dev 2.2.7-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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*
* This file is part of MIA - a toolbox for medical image analysis
* Copyright (c) Leipzig, Madrid 1999-2015 Gert Wollny
*
* MIA is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with MIA; if not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef mia_2d_transform_hh
#define mia_2d_transform_hh
#include <iterator>
#include <memory>
#include <ostream>
#include <mia/core/transformation.hh>
#include <mia/core/filter.hh>
#include <mia/2d/matrix.hh>
#include <mia/2d/image.hh>
#include <mia/2d/interpolator.hh>
NS_MIA_BEGIN
/**
@ingroup registration
\brief This is the generic base class for 2D transformations.
This class defines the generic interface for a 2D transformation.
Most methods are pure abstract and need to be implemented by a "real" transformation.
Actual implementations are provided as plug-ins.
*/
class EXPORT_2D C2DTransformation: public Transformation<C2DImage, C2DInterpolatorFactory> {
public:
/// generic name for the data used by this transformation
typedef C2DImage Data;
/// generic name for the size type used by this transformation
typedef C2DBounds Size;
/// generic name for the vector type used by this transformation
typedef C2DFVector Vector;
/// generic name for the interpolation factory used by this transformation
typedef C2DInterpolatorFactory InterpolatorFactory;
/// generic name for this transformation type
typedef C2DTransformation type;
/// pointer type of this transformation
typedef std::shared_ptr<C2DTransformation > Pointer;
/// plug-in search path element "type"
static const char *data_descr;
/// plug-in search path element "data"
static const char *dim_descr;
protected:
/**
@brief Base of the implementation of an iterator over the transformation domain
This iterator takes care of iterating over the transformation range. X is the fastest
changing index.
Some methods are abstract and must be defined in derived classes by using the
specific transformation model.
*/
class iterator_impl {
public:
iterator_impl();
/**
Constructor to initialize the iterator at a certain point
@param pos current position of the iterator
@param size defines the grid of the domain of the iterator as
\f$[0,size.x-1] \times [0,size.y-1]\f$
*/
iterator_impl(const C2DBounds& pos, const C2DBounds& size);
/// increment the position
void increment();
/// fast advance the position
void advance(unsigned int delta);
/// @returns the current value of the transformation iterated over
const C2DFVector& get_value() const;
/// @returns a dynamically allocated copy of the iterator
virtual iterator_impl * clone() const __attribute__((warn_unused_result)) = 0;
/**
Compare the iterator to another one
@param other
@returns true if the positions are equal or both are at the end of the range
@remark no test is run whether both iterator belong to the same transformation
*/
bool operator == (const iterator_impl& other) const;
/// @returns the cutrrent grid position of the iterator
const C2DBounds& get_pos()const;
/// @returns the domain size of the underlying transformation
const C2DBounds& get_size()const;
/**
Print some information about the iteratorto an output stream,
mostely used for debugging purpouses
@param os
*/
void print(std::ostream& os) const;
private:
virtual const C2DFVector& do_get_value()const = 0;
virtual void do_y_increment() = 0;
virtual void do_x_increment() = 0;
C2DBounds m_pos;
C2DBounds m_size;
};
public:
/**
Iterator to iterator over the grid points of the supported range
\todo this iterator shouldn't be here, but should be a separate
class not bound to the 2D transformation
*/
class const_iterator : public std::forward_iterator_tag {
public:
/// provide the STL with some typedef fro traits
typedef std::forward_iterator_tag iterator_category;
/// generic name for the value type of this iterator
typedef C2DFVector value_type;
/// generic name for the difference type of this iterator
typedef size_t difference_type;
/// generic name for the pointer type of this iterator
typedef C2DFVector *pointer;
/// generic name for the reference type of this iterator
typedef C2DFVector& reference;
/**
Standard constructor
\remark constructed like this the iterator is not usable.
*/
const_iterator();
/**
Constructor to be initialized with "a real implementation"
\param holder is the implementation that does all the real work
and depends on the transformation
*/
const_iterator(iterator_impl * holder);
/** Assignment operator implemnts the deep copy of the holder
The pointer to the holder is not shared but cloned.
*/
const_iterator& operator = (const const_iterator& other);
/** Copy Constructor impelemnts the deep copy of the holder
The pointer to the holder is not shared but cloned.
*/
const_iterator(const const_iterator& other);
/**
Prefix increment
*/
const_iterator& operator ++();
/**
Postfix increment
*/
const_iterator operator ++(int);
/**
Advance a certain amount of steps. This implementation
will ususlly be fatser than the generic std::advance function, since
for forward_iterators std::advance calls "++" delta times
@param delta
*/
const_iterator& operator += (unsigned int delta);
/// @returns the current value of the transformation
const C2DFVector& operator *() const;
/// @returns the pointer version of the current value of the transformation
const C2DFVector *operator ->() const;
const C2DBounds& pos() const;
const C2DBounds& get_size() const;
/** Print the current position and value to an output stream
\param os
*/
void print(std::ostream& os) const;
private:
std::unique_ptr<iterator_impl> m_holder;
friend EXPORT_2D bool operator == (const C2DTransformation::const_iterator& a,
const C2DTransformation::const_iterator& b);
};
using Transformation<C2DImage, C2DInterpolatorFactory>::operator ();
/**
Standard constructor place holder
*/
C2DTransformation(const C2DInterpolatorFactory& ipf);
/**
Set the descrition string that was used to create this transformstion
@param s
*/
void set_creator_string(const std::string& s);
/// \returns the description string used to create this transformations
const std::string& get_creator_string()const;
/**
\returns a newly allocated copy of the actual transformation
*/
virtual C2DTransformation *clone() const __attribute__((warn_unused_result));
/**
\returns a the inverse transform
*/
virtual C2DTransformation *invert() const __attribute__((warn_unused_result)) = 0;
/**
\returns the start iterator of the transformation that iterates over the grid
of the area the ransformation is defined on
*/
virtual const_iterator begin() const = 0;
/**
\returns the end iterator of the transformation that iterates over the grid
of the area the ransformation is defined on
*/
virtual const_iterator end() const = 0;
/**
Transforation upscaling to new image size
\param size new size of the transformation
\returns shared pointer to upscaled transformation
*/
Pointer upscale(const C2DBounds& size) const;
/**
update a transformation by using a vector field
\remark this is too specialized and should go away
*/
virtual void update(float step, const C2DFVectorfield& a) = 0;
/**
\returns the number of free parameters this transformation provides
*/
virtual size_t degrees_of_freedom() const = 0;
/**
set the transformation to be the identity transform
*/
virtual void set_identity() = 0;
/**
evaluate the derivative (Jacobian matrix) of the transformation at the given
coordinate
\param x
\returns 2x2 matrix of the derivative
*/
virtual C2DFMatrix derivative_at(const C2DFVector& x) const = 0;
/**
evaluate the derivative (Jacobian matrix) of the transformation at the given
grid coordinates
\param x
\param y
\returns 2x2 matrix of the derivative
*/
virtual C2DFMatrix derivative_at(int x, int y) const = 0;
/**
Translate the input gradient to a vector field in the space of the transformation field
\remark this is too specialized and needs to be replaced by something
*/
virtual void translate(const C2DFVectorfield& gradient, CDoubleVector& params) const = 0;
/**
\returns the transformation parameters as a flat value array
*/
virtual CDoubleVector get_parameters() const = 0;
/**
sets the transformation parameters from a flat value array
*/
virtual void set_parameters(const CDoubleVector& params) = 0;
/**
\returns the (approximate) maximum absolute translation of the transformation over the whole domain
*/
virtual float get_max_transform() const = 0;
/**
A transformation is defined on [0,X-1]x[0.Y-1].
\returns the upper boundaries (X,Y) of this range
*/
virtual const C2DBounds& get_size() const = 0;
/**
evaluate the pertuberation of a vectorfield combined with this transformation
\param[in,out] v vectorfield to be pertuberated
\returns maximum value of the pertuberation
\remark this makes only sense for fluid dynamics registration and should be handled elsewhere
*/
virtual float pertuberate(C2DFVectorfield& v) const = 0;
/**
\returns the displacement at coordinate x
\remark rename the function to something that explains better whats going on
*/
virtual C2DFVector apply(const C2DFVector& x) const = 0;
/**
apply the actual transformation to point x
\returns transformed point
*/
virtual C2DFVector operator () (const C2DFVector& x) const = 0;
/**
Evaluate the Jacobian of the transformation when updated with vector field v by factor delta
\returns Jacobian
\remark this only is used for fluid dynamics registration and should probably be moved elsewhere
*/
virtual float get_jacobian(const C2DFVectorfield& v, float delta) const = 0;
/**
If applicaple the transformation model is refined (e.g. splines
are converted to a denser coefficient distribution.
\returns \a true if refinement was applied, and \a false otherwise
*/
virtual bool refine();
/* Attributes */
/**
This attribute defines the voxel spacing of the input data of this transform.
*/
static constexpr const char *input_spacing_attr = "in-pixel-spacing";
/**
This attribute defines the output voxel spacing of this transform.
*/
static constexpr const char *output_spacing_attr = "out-pixel-spacing";
/**
\returns the minimal image size that makes sense for the transformation.
Usually this is (1,1), but for spline based transformation the image must
be larger.
*/
virtual C2DBounds get_minimal_supported_image_size() const;
private:
virtual Pointer do_upscale(const C2DBounds& size) const = 0;
std::string m_creator_string;
virtual C2DTransformation *do_clone() const __attribute__((warn_unused_result)) = 0;
P2DImage do_transform(const C2DImage& input, const C2DInterpolatorFactory& ipf) const;
};
/**
@ingroup registration
\brief Pointer type for the 2D transformation
*/
typedef C2DTransformation::Pointer P2DTransformation;
/**
@ingroup registration
\brief Move an 2D transformation iterator forward by using its provided += operator
don't use a reference to the iterator, because we use the created copy as result
*/
inline C2DTransformation::const_iterator operator + (C2DTransformation::const_iterator i, size_t delta)
{
i += delta;
return i;
}
/**
Print information about the iterator i to stream os (for debugging)
\param os
\param i
\returns os
*/
inline std::ostream& operator << (std::ostream& os,
const C2DTransformation::const_iterator& i)
{
i.print(os);
return os;
}
/**
@ingroup registration
\brief Compare two transformation iterators
\param a
\param b
\returns \a true if iterators are not equal, \a false otherwise
*/
EXPORT_2D bool operator != (const C2DTransformation::const_iterator& a,
const C2DTransformation::const_iterator& b);
NS_MIA_END
#endif
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