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thewtexthewtex
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Merge pull request #28 from richardbeare/ExtendedSeedsEdgeEffectsSquashed2
Extended seeds/way points and support for seeds on the edge of images.
2 parents 5a2017e + 7b31773 commit 21b01c8

34 files changed

+549
-63
lines changed

‎include/itkArrivalFunctionToPathFilter.h‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -180,6 +180,9 @@ class ITK_EXPORT ArrivalFunctionToPathFilter :
180180
typedef SingleValuedNonLinearOptimizer OptimizerType;
181181
typedef RegularStepGradientDescentOptimizer DefaultOptimizerType;
182182

183+
/** The points are in vectors to support extended "nodes" */
184+
typedef std::vector < PointType> PointsContainerType;
185+
183186
/** Get/set the Optimizer. */
184187
itkSetObjectMacro( Optimizer, OptimizerType );
185188
itkGetConstObjectMacro( Optimizer, OptimizerType );
@@ -226,12 +229,12 @@ class ITK_EXPORT ArrivalFunctionToPathFilter :
226229
virtual InputImageType * ComputeArrivalFunction( );
227230

228231
/** Get the next end point from which to back propagate. */
229-
virtual const PointType & GetNextEndPoint( );
232+
virtual const PointsContainerType & GetNextEndPoint( );
230233

231234
typename CostFunctionType::Pointer m_CostFunction;
232235
typename OptimizerType::Pointer m_Optimizer;
233236
typename OptimizerType::MeasureType m_TerminationValue;
234-
std::vector<PointType> m_PointList;
237+
std::vector<PointsContainerType> m_PointList;
235238
unsigned int m_CurrentOutput;
236239

237240
private:

‎include/itkArrivalFunctionToPathFilter.hxx‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -53,7 +53,9 @@ void
5353
ArrivalFunctionToPathFilter<TInputImage,TOutputPath>
5454
::AddPathEndPoint(const PointType &point)
5555
{
56-
m_PointList.push_back( point );
56+
PointsContainerType V(1);
57+
V[0] = point;
58+
m_PointList.push_back( V );
5759
this->Modified();
5860
}
5961

@@ -95,7 +97,7 @@ ArrivalFunctionToPathFilter<TInputImage,TOutputPath>
9597
}
9698

9799
template<class TInputImage, class TOutputPath>
98-
const typename ArrivalFunctionToPathFilter<TInputImage,TOutputPath>::PointType &
100+
const typename ArrivalFunctionToPathFilter<TInputImage,TOutputPath>::PointsContainerType &
99101
ArrivalFunctionToPathFilter<TInputImage,TOutputPath>
100102
::GetNextEndPoint()
101103
{
@@ -190,7 +192,8 @@ ArrivalFunctionToPathFilter<TInputImage,TOutputPath>
190192
}
191193

192194
// Get the end point to back propagate from
193-
PointType pointEnd = this->GetNextEndPoint();
195+
PointsContainerType allpoints = this->GetNextEndPoint();
196+
PointType pointEnd = allpoints[0];
194197

195198
// Convert end point to parameters type
196199
typename CostFunctionType::ParametersType end(InputImageDimension);

‎include/itkSingleImageCostFunction.h‎

Lines changed: 16 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -128,6 +128,18 @@ class ITK_EXPORT SingleImageCostFunction :
128128
virtual void GetDerivative( const ParametersType & parameters,
129129
DerivativeType & derivative ) const ITK_OVERRIDE;
130130

131+
// Set these depending on whether you will be minimizing or maximizing.
132+
// They control the value returned when the point isn't inside the buffer.
133+
void SetMinimize()
134+
{
135+
m_OutsideValue = itk::NumericTraits< ImagePixelType >::max();
136+
}
137+
void SetMaximize()
138+
{
139+
m_OutsideValue = itk::NumericTraits< ImagePixelType >::NonpositiveMin();
140+
}
141+
142+
131143
protected:
132144
SingleImageCostFunction();
133145
virtual ~SingleImageCostFunction() {}
@@ -139,7 +151,10 @@ class ITK_EXPORT SingleImageCostFunction :
139151
ImageConstPointer m_Image;
140152
typename InterpolatorType::Pointer m_Interpolator;
141153
typename GradientImageFunctionType::Pointer m_GradientImageFunction;
142-
154+
/** Used to define the value outside the image buffer. Important when
155+
* path points are on the edge of an image */
156+
ImagePixelType m_OutsideValue;
157+
143158
};
144159

145160
} // end namespace itk

‎include/itkSingleImageCostFunction.hxx‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -72,6 +72,7 @@ SingleImageCostFunction<TImage>
7272
m_Interpolator->SetInputImage( m_Image );
7373
m_GradientImageFunction->SetInputImage( m_Image );
7474

75+
this->SetMinimize();
7576
// If there are any objects observing the cost function,
7677
// call them to give the user code a chance to set parameters
7778
this->InvokeEvent( InitializeEvent() );
@@ -101,7 +102,7 @@ SingleImageCostFunction<TImage>
101102
}
102103
else
103104
{
104-
return 0.0;
105+
return m_OutsideValue;
105106
}
106107
}
107108

‎include/itkSpeedFunctionPathInformation.h‎

Lines changed: 43 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -29,6 +29,10 @@ namespace itk
2929
* \brief PathInfo class for encapsulating information about a path
3030
* for a SpeedFunctionToPathFilter Object.
3131
* The points are stored as follows: end, start, way0, way1, ..., wayN.
32+
* Each element of a path can be a set of points - e.g. "end" may be
33+
* derived from a segmentation mask. Alternatively start and end may
34+
* be the left and right sides of a 2d image, producing a minimal
35+
* path across the image.
3236
* Fronts are propagated in reverse order: wayN, ..., way1, way0, start.
3337
* (NOTE: a front is never propagated from end).
3438
*
@@ -55,14 +59,16 @@ class SpeedFunctionPathInformation :
5559
typedef SmartPointer<Self> Pointer;
5660
typedef SmartPointer<const Self> ConstPointer;
5761

62+
5863
/** Run-time type information (and related methods). */
5964
itkTypeMacro(SpeedFunctionPathInformation, LightObject);
6065

6166
/** Method for creation through the object factory. */
6267
itkNewMacro(Self);
6368

6469
/** Some point typedefs. */
65-
typedef TPoint PointType;
70+
typedef TPoint PointType;
71+
typedef std::vector< PointType > PointsContainerType;
6672

6773
void ClearInfo();
6874

@@ -72,34 +78,60 @@ class SpeedFunctionPathInformation :
7278

7379
void AddWayPoint( const PointType & way );
7480

81+
82+
/** Methods for adding extended path components **/
83+
void SetStartPoint( const PointsContainerType & start );
84+
85+
void SetEndPoint( const PointsContainerType & end );
86+
87+
void AddWayPoint( const PointsContainerType & way );
88+
89+
// methods for modifying path seeds - needed when using
90+
// an extended seed.
91+
void SetCurrent( const PointsContainerType & newcurrent );
92+
void SetPrevious( const PointsContainerType & newprevious );
93+
void SetNext( const PointsContainerType & newnext );
94+
95+
void SetCurrent( const PointType & current );
96+
void SetPrevious( const PointType & newprevious );
97+
void SetNext( const PointType & newnext );
98+
99+
void Advance();
100+
75101
unsigned int GetNumberOfPoints( ) const;
76102

77-
const PointType & GetStartPoint( ) const;
103+
const PointsContainerType & GetStartPoint( ) const;
78104

79-
const PointType & GetEndPoint( ) const;
105+
const PointsContainerType & GetEndPoint( ) const;
80106

81-
const PointType & GetWayPoint( SizeValueType i ) const;
107+
const PointsContainerType & GetWayPoint( SizeValueType i ) const;
82108

83109
bool HasNextFront( ) const;
84110

85-
const PointType & GetCurrentFrontAndAdvance( );
86-
87-
const PointType & PeekCurrentFront( ) const;
111+
const PointsContainerType & GetCurrentFrontAndAdvance( );
88112

89-
const PointType & PeekNextFront( ) const;
113+
const PointsContainerType & PeekCurrentFront( ) const;
90114

91-
const PointType & PeekPreviousFront( ) const;
115+
const PointsContainerType & PeekNextFront( ) const;
92116

117+
const PointsContainerType & PeekPreviousFront( ) const;
118+
93119

94120
protected:
95121
SpeedFunctionPathInformation( );
96122
virtual ~SpeedFunctionPathInformation( );
97123
virtual void PrintSelf( std::ostream& os, Indent indent ) const ITK_OVERRIDE;
98124

99-
std::vector< PointType > m_Information;
100-
SizeValueType m_Front;
125+
std::vector< PointsContainerType > m_Information;
126+
SizeValueType m_Front;
101127

102128

129+
PointsContainerType PtoPVec(const PointType & P)
130+
{
131+
PointsContainerType V(1);
132+
V[0]=P;
133+
return(V);
134+
}
103135
private:
104136
ITK_DISALLOW_COPY_AND_ASSIGN(SpeedFunctionPathInformation);
105137
};

‎include/itkSpeedFunctionPathInformation.hxx‎

Lines changed: 99 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -52,26 +52,116 @@ template <typename TPoint>
5252
void SpeedFunctionPathInformation<TPoint>
5353
::SetStartPoint( const PointType & start )
5454
{
55-
m_Information[1] = start;
55+
m_Information[1] = PtoPVec(start);
5656
}
5757

5858

5959
template <typename TPoint>
6060
void SpeedFunctionPathInformation<TPoint>
6161
::SetEndPoint( const PointType & end )
6262
{
63-
m_Information[0] = end;
63+
m_Information[0] = PtoPVec( end );
6464
}
6565

6666

6767
template <typename TPoint>
6868
void SpeedFunctionPathInformation<TPoint>
6969
::AddWayPoint( const PointType & way )
70+
{
71+
m_Information.push_back( PtoPVec(way) );
72+
m_Front++;
73+
}
74+
75+
template <typename TPoint>
76+
void SpeedFunctionPathInformation<TPoint>
77+
::SetCurrent( const PointType & newcurrent )
78+
{
79+
m_Information[m_Front] = PtoPVec(newcurrent);
80+
}
81+
82+
template <typename TPoint>
83+
void SpeedFunctionPathInformation<TPoint>
84+
::Advance( void )
85+
{
86+
m_Front--;
87+
}
88+
89+
template <typename TPoint>
90+
void SpeedFunctionPathInformation<TPoint>
91+
::SetStartPoint( const PointsContainerType & start )
92+
{
93+
m_Information[1] = start;
94+
}
95+
96+
97+
template <typename TPoint>
98+
void SpeedFunctionPathInformation<TPoint>
99+
::SetEndPoint( const PointsContainerType & end )
100+
{
101+
m_Information[0] = end;
102+
}
103+
104+
105+
template <typename TPoint>
106+
void SpeedFunctionPathInformation<TPoint>
107+
::AddWayPoint( const PointsContainerType & way )
70108
{
71109
m_Information.push_back( way );
72110
m_Front++;
73111
}
74112

113+
template <typename TPoint>
114+
void SpeedFunctionPathInformation<TPoint>
115+
::SetCurrent( const PointsContainerType & newcurrent )
116+
{
117+
m_Information[m_Front] = newcurrent;
118+
}
119+
120+
template <typename TPoint>
121+
void SpeedFunctionPathInformation<TPoint>
122+
::SetPrevious( const PointsContainerType & newprevious )
123+
{
124+
SizeValueType F;
125+
if ( m_Front == m_Information.size()-1 )
126+
{
127+
F=0;
128+
}
129+
else
130+
{
131+
F = m_Front+1;
132+
}
133+
m_Information[F] = newprevious;
134+
}
135+
template <typename TPoint>
136+
void SpeedFunctionPathInformation<TPoint>
137+
::SetNext( const PointsContainerType & newnext )
138+
{
139+
SizeValueType F;
140+
if (m_Front <= 1)
141+
{
142+
F=1;
143+
}
144+
else
145+
{
146+
F = m_Front - 1;
147+
}
148+
m_Information[F] = newnext;
149+
}
150+
151+
template <typename TPoint>
152+
void SpeedFunctionPathInformation<TPoint>
153+
::SetPrevious( const PointType & newprevious )
154+
{
155+
SetPrevious(PtoPVec(newprevious));
156+
}
157+
158+
template <typename TPoint>
159+
void SpeedFunctionPathInformation<TPoint>
160+
::SetNext( const PointType & newnext )
161+
{
162+
SetNext(PtoPVec(newnext));
163+
}
164+
75165

76166
template <typename TPoint>
77167
unsigned int SpeedFunctionPathInformation<TPoint>
@@ -82,7 +172,7 @@ unsigned int SpeedFunctionPathInformation<TPoint>
82172

83173

84174
template <typename TPoint>
85-
const typename SpeedFunctionPathInformation<TPoint>::PointType &
175+
const typename SpeedFunctionPathInformation<TPoint>::PointsContainerType &
86176
SpeedFunctionPathInformation<TPoint>
87177
::GetStartPoint( ) const
88178
{
@@ -91,7 +181,7 @@ SpeedFunctionPathInformation<TPoint>
91181

92182

93183
template <typename TPoint>
94-
const typename SpeedFunctionPathInformation<TPoint>::PointType &
184+
const typename SpeedFunctionPathInformation<TPoint>::PointsContainerType &
95185
SpeedFunctionPathInformation<TPoint>
96186
::GetEndPoint( ) const
97187
{
@@ -100,7 +190,7 @@ SpeedFunctionPathInformation<TPoint>
100190

101191

102192
template <typename TPoint>
103-
const typename SpeedFunctionPathInformation<TPoint>::PointType &
193+
const typename SpeedFunctionPathInformation<TPoint>::PointsContainerType &
104194
SpeedFunctionPathInformation<TPoint>
105195
::GetWayPoint( SizeValueType i ) const
106196
{
@@ -118,7 +208,7 @@ bool SpeedFunctionPathInformation<TPoint>
118208

119209

120210
template <typename TPoint>
121-
const typename SpeedFunctionPathInformation<TPoint>::PointType &
211+
const typename SpeedFunctionPathInformation<TPoint>::PointsContainerType &
122212
SpeedFunctionPathInformation<TPoint>
123213
::GetCurrentFrontAndAdvance( )
124214
{
@@ -127,7 +217,7 @@ SpeedFunctionPathInformation<TPoint>
127217

128218

129219
template <typename TPoint>
130-
const typename SpeedFunctionPathInformation<TPoint>::PointType &
220+
const typename SpeedFunctionPathInformation<TPoint>::PointsContainerType &
131221
SpeedFunctionPathInformation<TPoint>
132222
::PeekCurrentFront( ) const
133223
{
@@ -136,7 +226,7 @@ SpeedFunctionPathInformation<TPoint>
136226

137227

138228
template <typename TPoint>
139-
const typename SpeedFunctionPathInformation<TPoint>::PointType &
229+
const typename SpeedFunctionPathInformation<TPoint>::PointsContainerType &
140230
SpeedFunctionPathInformation<TPoint>
141231
::PeekNextFront( ) const
142232
{
@@ -152,7 +242,7 @@ SpeedFunctionPathInformation<TPoint>
152242

153243

154244
template <typename TPoint>
155-
const typename SpeedFunctionPathInformation<TPoint>::PointType &
245+
const typename SpeedFunctionPathInformation<TPoint>::PointsContainerType &
156246
SpeedFunctionPathInformation<TPoint>
157247
::PeekPreviousFront( ) const
158248
{

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