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3d/transform.hh
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1/* -*- mia-c++ -*-
2 *
3 * This file is part of MIA - a toolbox for medical image analysis
4 * Copyright (c) Leipzig, Madrid 1999-2017 Gert Wollny
5 *
6 * MIA is free software; you can redistribute it and/or modify
7 * it under the terms of the GNU General Public License as published by
8 * the Free Software Foundation; either version 3 of the License, or
9 * (at your option) any later version.
10 *
11 * This program is distributed in the hope that it will be useful,
12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 * GNU General Public License for more details.
15 *
16 * You should have received a copy of the GNU General Public License
17 * along with MIA; if not, see <http://www.gnu.org/licenses/>.
18 *
19 */
20
21#ifndef mia_3d_transform_hh
22#define mia_3d_transform_hh
23
24#include <iterator>
25#include <memory>
26
27#include <mia/core/vector.hh>
29#include <mia/core/filter.hh>
30#include <mia/3d/matrix.hh>
31#include <mia/3d/image.hh>
33
35
36
38
43typedef std::shared_ptr<C3DTransformation > P3DTransformation;
44
53class EXPORT_3D C3DTransformation: public Transformation<C3DImage, C3DInterpolatorFactory>
54{
55public:
57 typedef C3DBounds Size;
58 typedef C3DImage Data;
59 typedef C3DFVector Vector;
61 typedef C3DTransformation type;
62 typedef std::shared_ptr<C3DTransformation> Pointer;
63 static const char *data_descr;
64 static const char *dim_descr;
66protected:
71 {
72 public:
74
80 iterator_impl(const C3DBounds& pos, const C3DBounds& size);
81
89 iterator_impl(const C3DBounds& pos, const C3DBounds& begin,
90 const C3DBounds& end, const C3DBounds& size);
91
93 void increment();
94
96 const C3DFVector& get_value() const;
97
99 virtual iterator_impl *clone() const __attribute__((warn_unused_result)) = 0;
100
105 bool operator == (const iterator_impl& other) const;
106
108 const C3DBounds& get_pos()const;
109
111 const C3DBounds& get_size()const;
112 private:
113 virtual const C3DFVector& do_get_value()const = 0;
114 virtual void do_z_increment() = 0;
115 virtual void do_y_increment() = 0;
116 virtual void do_x_increment() = 0;
117
118 C3DBounds m_pos;
119 C3DBounds m_size;
120 C3DBounds m_start;
121 C3DBounds m_end;
122
123
124 };
125public:
134 class const_iterator : public std::forward_iterator_tag
135 {
136 public:
137
139 typedef std::forward_iterator_tag iterator_category;
140 typedef C3DFVector value_type;
141 typedef size_t difference_type;
142 typedef C3DFVector *pointer;
143 typedef C3DFVector& reference;
145
147
150
153
155 const_iterator& operator = (const const_iterator& other);
156
158 const_iterator& operator ++();
159
161 const_iterator operator ++(int);
162
164 const C3DFVector& operator *() const;
165
167 const C3DFVector *operator ->() const;
168
170 const C3DBounds& pos()const;
171
172
174 const C3DBounds& get_size()const;
175
176
177 private:
178 std::unique_ptr<iterator_impl> m_holder;
179
182
183 };
184
185
187
192
197 void set_creator_string(const std::string& s);
198
200 const std::string& get_creator_string()const;
201
205 virtual C3DTransformation *clone() const;
206
210 virtual C3DTransformation *invert() const = 0;
211
212
217 virtual const_iterator begin() const = 0;
218
224 virtual const_iterator end() const = 0;
225
226
231 virtual const_iterator begin_range(const C3DBounds& begin, const C3DBounds& end) const = 0;
232
238 virtual const_iterator end_range(const C3DBounds& begin, const C3DBounds& end) const = 0;
239
244 virtual void reinit() const;
245
246
253
258 virtual void update(float step, const C3DFVectorfield& a) = 0;
259
263 virtual size_t degrees_of_freedom() const = 0;
264
268 virtual void set_identity() = 0;
269
278 virtual C3DFMatrix derivative_at(int x, int y, int z) const = 0;
279
286 virtual C3DFMatrix derivative_at(const C3DFVector& x) const = 0;
287
292 virtual void translate(const C3DFVectorfield& gradient, CDoubleVector& params) const = 0;
293
297 virtual CDoubleVector get_parameters() const = 0;
298
302 virtual void set_parameters(const CDoubleVector& params) = 0;
303
307 virtual float get_max_transform() const = 0;
308
313 virtual const C3DBounds& get_size() const = 0;
314
321 virtual float pertuberate(C3DFVectorfield& v) const = 0;
322
327 virtual C3DFVector apply(const C3DFVector& x) const __attribute__((deprecated));
328
335 virtual C3DFVector get_displacement_at(const C3DFVector& x) const = 0;
336
341 virtual C3DFVector operator () (const C3DFVector& x) const = 0;
342
348 virtual float get_jacobian(const C3DFVectorfield& v, float delta) const = 0;
349
356 virtual bool refine();
357
361 void set_debug();
362
363 /* Attributes */
367 static constexpr const char *input_spacing_attr = "in-voxel-spacing";
368
372 static constexpr const char *output_spacing_attr = "out-voxel-spacing";
373
374
376protected:
378 bool get_debug()const;
379
380private:
381 P3DImage do_transform(const C3DImage& input, const C3DInterpolatorFactory& ipf) const;
382
383 virtual P3DTransformation do_upscale(const C3DBounds& size) const = 0;
384
385 std::string m_creator_string;
386 virtual C3DTransformation *do_clone() const = 0;
387 bool m_debug;
388};
389
390
401
402
404
405#endif
C3DImage::Pointer P3DImage
define a shortcut to the 3D image shared pointer.
Definition: 3d/image.hh:135
bool operator==(const CAttribute &a, const CAttribute &b)
Definition: attributes.hh:95
a 3D field of floating point single accuracy 3D vectors
The generic base type of a 3D image.
Definition: 3d/image.hh:47
A factory to create interpolators of a given type by providing input data.
const C3DBounds & pos() const
return the current position in 3D space
const_iterator(iterator_impl *holder)
initialize the iterator with the actual worker object
const C3DBounds & get_size() const
const_iterator(const const_iterator &other)
Copy constructor.
virtual iterator_impl * clone() const __attribute__((warn_unused_result))=0
const C3DFVector & get_value() const
void increment()
move to next position
iterator_impl(const C3DBounds &pos, const C3DBounds &begin, const C3DBounds &end, const C3DBounds &size)
iterator_impl(const C3DBounds &pos, const C3DBounds &size)
This is the generic base class for 3D transformations.
Definition: 3d/transform.hh:54
virtual float get_jacobian(const C3DFVectorfield &v, float delta) const =0
C3DTransformation(const C3DInterpolatorFactory &ipf)
virtual C3DFVector apply(const C3DFVector &x) const __attribute__((deprecated))
virtual void update(float step, const C3DFVectorfield &a)=0
virtual float pertuberate(C3DFVectorfield &v) const =0
virtual void set_parameters(const CDoubleVector &params)=0
virtual const_iterator begin() const =0
virtual float get_max_transform() const =0
P3DTransformation upscale(const C3DBounds &size) const
void set_creator_string(const std::string &s)
virtual C3DBounds get_minimal_supported_image_size() const
virtual C3DTransformation * invert() const =0
virtual void set_identity()=0
virtual C3DFMatrix derivative_at(int x, int y, int z) const =0
virtual bool refine()
virtual C3DFMatrix derivative_at(const C3DFVector &x) const =0
virtual void reinit() const
virtual CDoubleVector get_parameters() const =0
virtual size_t degrees_of_freedom() const =0
bool get_debug() const
virtual void translate(const C3DFVectorfield &gradient, CDoubleVector &params) const =0
const std::string & get_creator_string() const
virtual const_iterator end() const =0
virtual const C3DBounds & get_size() const =0
virtual const_iterator end_range(const C3DBounds &begin, const C3DBounds &end) const =0
virtual const_iterator begin_range(const C3DBounds &begin, const C3DBounds &end) const =0
virtual C3DTransformation * clone() const
virtual C3DFVector get_displacement_at(const C3DFVector &x) const =0
A wrapper around the c-array to provide an STL like interface for iterators.
Definition: core/vector.hh:78
generic base class for transformations
I InterpolatorFactory
type of the interpolator used by this transformation
D Data
typedef for the data type to be transformed by this transformation
#define EXPORT_3D
Definition: defines3d.hh:45
#define NS_MIA_BEGIN
conveniance define to start the mia namespace
Definition: defines.hh:33
#define NS_MIA_END
conveniance define to end the mia namespace
Definition: defines.hh:36
EXPORT_3D bool operator!=(const C3DTransformation::const_iterator &a, const C3DTransformation::const_iterator &b)
Compare two transformation iterators.
std::shared_ptr< C3DTransformation > P3DTransformation
pointer type for a 3D transformation
Definition: 3d/transform.hh:43
Matrix EXPORT_GSL operator*(const Matrix &lhs, const Matrix &rhs)