1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
|
#!/usr/bin/env python
## Program: VMTK
## Module: $RCSfile: vmtkimagefeatures.py,v $
## Language: Python
## Date: $Date: 2006/07/17 09:53:14 $
## Version: $Revision: 1.8 $
## Copyright (c) Luca Antiga, David Steinman. All rights reserved.
## See LICENCE file for details.
## This software is distributed WITHOUT ANY WARRANTY; without even
## the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
## PURPOSE. See the above copyright notices for more information.
import vtk
import sys
import pypes
import vtkvmtk
vmtkimagefeatures = 'vmtkImageFeatures'
class vmtkImageFeatures(pypes.pypeScript):
def __init__(self):
pypes.pypeScript.__init__(self)
self.Image = None
self.FeatureImage = None
self.Dimensionality = 3
self.DerivativeSigma = 0.0
self.SigmoidRemapping = 0
self.FeatureImageType = 'gradient'
self.UpwindFactor = 1.0
self.FWHMRadius = [3, 3, 3]
self.FWHMBackgroundValue = 0.0
self.SetScriptName('vmtkimagefeatures')
self.SetScriptDoc('compute a feature image for use in segmentation')
self.SetInputMembers([
['Image','i','vtkImageData',1,'','the input image','vmtkimagereader'],
['FeatureImageType','featureimagetype','str',1,'["vtkgradient","gradient","upwind","fwhm"]'],
['Dimensionality','dimensionality','int',1,'(2,3,1)'],
['SigmoidRemapping','sigmoid','bool',1],
['DerivativeSigma','derivativesigma','float',1,'(0.0,)'],
['UpwindFactor','upwindfactor','float',1,'(0.0,1.0)'],
['FWHMRadius','fwhmradius','int',3,'(0,)'],
['FWHMBackgroundValue','fwhmbackgroundvalue','float',1]
])
self.SetOutputMembers([
['Image','o','vtkImageData',1,'','the output image','vmtkimagewriter']
])
def BuildVTKGradientBasedFeatureImage(self):
cast = vtk.vtkImageCast()
cast.SetInput(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
gradientMagnitude = vtk.vtkImageGradientMagnitude()
gradientMagnitude.SetInput(cast.GetOutput())
gradientMagnitude.SetDimensionality(self.Dimensionality)
gradientMagnitude.Update()
imageAdd = vtk.vtkImageMathematics()
imageAdd.SetInput(gradientMagnitude.GetOutput())
imageAdd.SetOperationToAddConstant()
imageAdd.SetConstantC(1.0)
imageAdd.Update()
imageInvert = vtk.vtkImageMathematics()
imageInvert.SetInput(imageAdd.GetOutput())
imageInvert.SetOperationToInvert()
imageInvert.SetConstantC(1E20)
imageInvert.DivideByZeroToCOn()
imageInvert.Update()
self.FeatureImage = vtk.vtkImageData()
self.FeatureImage.DeepCopy(imageInvert.GetOutput())
self.FeatureImage.Update()
def BuildFWHMBasedFeatureImage(self):
cast = vtk.vtkImageCast()
cast.SetInput(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
fwhmFeatureImageFilter = vtkvmtk.vtkvmtkFWHMFeatureImageFilter()
fwhmFeatureImageFilter.SetInput(cast.GetOutput())
fwhmFeatureImageFilter.SetRadius(self.FWHMRadius)
fwhmFeatureImageFilter.SetBackgroundValue(self.FWHMBackgroundValue)
fwhmFeatureImageFilter.Update()
self.FeatureImage = vtk.vtkImageData()
self.FeatureImage.DeepCopy(fwhmFeatureImageFilter.GetOutput())
self.FeatureImage.Update()
def BuildUpwindGradientBasedFeatureImage(self):
cast = vtk.vtkImageCast()
cast.SetInput(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
gradientMagnitude = vtkvmtk.vtkvmtkUpwindGradientMagnitudeImageFilter()
gradientMagnitude.SetInput(cast.GetOutput())
gradientMagnitude.SetUpwindFactor(self.UpwindFactor)
gradientMagnitude.Update()
featureImage = None
if self.SigmoidRemapping==1:
scalarRange = gradientMagnitude.GetOutput().GetPointData().GetScalars().GetRange()
inputMinimum = scalarRange[0]
inputMaximum = scalarRange[1]
alpha = - (inputMaximum - inputMinimum) / 6.0
beta = (inputMaximum + inputMinimum) / 2.0
sigmoid = vtkvmtk.vtkvmtkSigmoidImageFilter()
sigmoid.SetInput(gradientMagnitude.GetOutput())
sigmoid.SetAlpha(alpha)
sigmoid.SetBeta(beta)
sigmoid.SetOutputMinimum(0.0)
sigmoid.SetOutputMaximum(1.0)
sigmoid.Update()
featureImage = sigmoid.GetOutput()
else:
boundedReciprocal = vtkvmtk.vtkvmtkBoundedReciprocalImageFilter()
boundedReciprocal.SetInput(gradientMagnitude.GetOutput())
boundedReciprocal.Update()
featureImage = boundedReciprocal.GetOutput()
self.FeatureImage = vtk.vtkImageData()
self.FeatureImage.DeepCopy(featureImage)
self.FeatureImage.Update()
def BuildGradientBasedFeatureImage(self):
cast = vtk.vtkImageCast()
cast.SetInput(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
if (self.DerivativeSigma > 0.0):
gradientMagnitude = vtkvmtk.vtkvmtkGradientMagnitudeRecursiveGaussianImageFilter()
gradientMagnitude.SetInput(cast.GetOutput())
gradientMagnitude.SetSigma(self.DerivativeSigma)
gradientMagnitude.SetNormalizeAcrossScale(0)
gradientMagnitude.Update()
else:
gradientMagnitude = vtkvmtk.vtkvmtkGradientMagnitudeImageFilter()
gradientMagnitude.SetInput(cast.GetOutput())
gradientMagnitude.Update()
featureImage = None
if self.SigmoidRemapping==1:
scalarRange = gradientMagnitude.GetOutput().GetPointData().GetScalars().GetRange()
inputMinimum = scalarRange[0]
inputMaximum = scalarRange[1]
alpha = - (inputMaximum - inputMinimum) / 6.0
beta = (inputMaximum + inputMinimum) / 2.0
sigmoid = vtkvmtk.vtkvmtkSigmoidImageFilter()
sigmoid.SetInput(gradientMagnitude.GetOutput())
sigmoid.SetAlpha(alpha)
sigmoid.SetBeta(beta)
sigmoid.SetOutputMinimum(0.0)
sigmoid.SetOutputMaximum(1.0)
sigmoid.Update()
featureImage = sigmoid.GetOutput()
else:
boundedReciprocal = vtkvmtk.vtkvmtkBoundedReciprocalImageFilter()
boundedReciprocal.SetInput(gradientMagnitude.GetOutput())
boundedReciprocal.Update()
featureImage = boundedReciprocal.GetOutput()
self.FeatureImage = vtk.vtkImageData()
self.FeatureImage.DeepCopy(featureImage)
self.FeatureImage.Update()
def Execute(self):
if self.Image == None:
self.PrintError('Error: No input image.')
if self.FeatureImageType == 'vtkgradient':
self.BuildVTKGradientBasedFeatureImage()
elif self.FeatureImageType == 'gradient':
self.BuildGradientBasedFeatureImage()
elif self.FeatureImageType == 'upwind':
self.BuildUpwindGradientBasedFeatureImage()
elif self.FeatureImageType == 'fwhm':
self.BuildFWHMBasedFeatureImage()
else:
self.PrintError('Error: unsupported feature image type')
self.Image = self.FeatureImage
if __name__=='__main__':
main = pypes.pypeMain()
main.Arguments = sys.argv
main.Execute()
|
