ITK  6.0.0
Insight Toolkit
itkDiffusionTensor3DReconstructionImageFilter.h
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1/*=========================================================================
2 *
3 * Copyright NumFOCUS
4 *
5 * Licensed under the Apache License, Version 2.0 (the "License");
6 * you may not use this file except in compliance with the License.
7 * You may obtain a copy of the License at
8 *
9 * https://www.apache.org/licenses/LICENSE-2.0.txt
10 *
11 * Unless required by applicable law or agreed to in writing, software
12 * distributed under the License is distributed on an "AS IS" BASIS,
13 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
14 * See the License for the specific language governing permissions and
15 * limitations under the License.
16 *
17 *=========================================================================*/
18#ifndef itkDiffusionTensor3DReconstructionImageFilter_h
19#define itkDiffusionTensor3DReconstructionImageFilter_h
20
22#include "itkSpatialObject.h"
24#include "vnl/vnl_matrix.h"
25#include "vnl/vnl_vector_fixed.h"
26#include "vnl/vnl_matrix_fixed.h"
27#include "vnl/algo/vnl_svd.h"
28#include "itkVectorContainer.h"
29#include "itkVectorImage.h"
30#include "ITKDiffusionTensorImageExport.h"
31
32namespace itk
33{
39{
40public:
45 enum class GradientImageFormat : uint8_t
46 {
47 GradientIsInASingleImage = 1,
48 GradientIsInManyImages,
49 Else
50 };
51};
52// Define how to print enumeration
53extern ITKDiffusionTensorImage_EXPORT std::ostream &
55
145template <typename TReferenceImagePixelType,
146 typename TGradientImagePixelType = TReferenceImagePixelType,
147 typename TTensorPixelType = double,
148 typename TMaskImageType = Image<unsigned char, 3>>
150 : public ImageToImageFilter<Image<TReferenceImagePixelType, 3>, Image<DiffusionTensor3D<TTensorPixelType>, 3>>
151{
152public:
158
160 itkNewMacro(Self);
161
163 itkOverrideGetNameOfClassMacro(DiffusionTensor3DReconstructionImageFilter);
164
165 using ReferencePixelType = TReferenceImagePixelType;
166
167 using GradientPixelType = TGradientImagePixelType;
168
170
173 using ReferenceImageType = typename Superclass::InputImageType;
174
176
178
179 using typename Superclass::OutputImageRegionType;
180
183
189
192
194 using MaskImageType = TMaskImageType;
195
197 using TensorBasisMatrixType = vnl_matrix_fixed<double, 6, 6>;
198
199 using CoefficientMatrixType = vnl_matrix<double>;
200
202 using GradientDirectionType = vnl_vector_fixed<double, 3>;
203
206
208 void
210 const GradientImageType *
211 GetGradientImage(unsigned int index) const;
220 void
222
224 void
226 {
227 if (m_GradientImageTypeEnumeration ==
229 {
230 itkExceptionMacro("Cannot call both methods:"
231 << "AddGradientImage and SetGradientImage. Please call only one of them.");
232 }
233
234 this->ProcessObject::SetNthInput(0, referenceImage);
235
236 m_GradientImageTypeEnumeration =
238 }
239
241 virtual ReferenceImageType *
243 {
244 return (static_cast<ReferenceImageType *>(this->ProcessObject::GetInput(0)));
245 }
246
248 virtual GradientDirectionType
249 GetGradientDirection(unsigned int idx) const
250 {
251 if (idx >= m_NumberOfGradientDirections)
252 {
253 itkExceptionMacro("Gradient direction " << idx << " does not exist");
254 }
255 return m_GradientDirectionContainer->ElementAt(idx);
256 }
260 void
262
264 void
266
267
271 itkSetMacro(Threshold, ReferencePixelType);
272 itkGetConstMacro(Threshold, ReferencePixelType);
281 itkSetMacro(BValue, TTensorPixelType);
282#ifdef GetBValue
283# undef GetBValue
284#endif
285 itkGetConstReferenceMacro(BValue, TTensorPixelType);
288#ifdef ITK_USE_CONCEPT_CHECKING
289 // Begin concept checking
290 itkConceptMacro(ReferenceEqualityComparableCheck, (Concept::EqualityComparable<ReferencePixelType>));
291 itkConceptMacro(TensorEqualityComparableCheck, (Concept::EqualityComparable<TensorPixelType>));
292 itkConceptMacro(GradientConvertibleToDoubleCheck, (Concept::Convertible<GradientPixelType, double>));
293 itkConceptMacro(DoubleConvertibleToTensorCheck, (Concept::Convertible<double, TensorPixelType>));
294 itkConceptMacro(GradientReferenceAdditiveOperatorsCheck,
296 itkConceptMacro(GradientReferenceAdditiveAndAssignOperatorsCheck,
298
299 itkConceptMacro(ReferenceOStreamWritableCheck, (Concept::OStreamWritable<ReferencePixelType>));
300 itkConceptMacro(TensorOStreamWritableCheck, (Concept::OStreamWritable<TensorPixelType>));
301 // End concept checking
302#endif
303
304protected:
307 void
308 PrintSelf(std::ostream & os, Indent indent) const override;
309
310 void
312
313 void
315
316 void
317 DynamicThreadedGenerateData(const OutputImageRegionType & outputRegionForThread) override;
318
319 void
320 VerifyPreconditions() const override;
321
324#if !defined(ITK_LEGACY_REMOVE)
325 // We need to expose the enum values at the class level
326 // for backwards compatibility
327 static constexpr GradientImageTypeEnumeration GradientIsInASingleImage =
328 GradientImageTypeEnumeration::GradientIsInASingleImage;
329 static constexpr GradientImageTypeEnumeration GradientIsInManyImages =
330 GradientImageTypeEnumeration::GradientIsInManyImages;
331 static constexpr GradientImageTypeEnumeration Else = GradientImageTypeEnumeration::Else;
332#endif
333
334private:
335 /* Tensor basis coeffs */
336 TensorBasisMatrixType m_TensorBasis{};
337
339
341 GradientDirectionContainerType::Pointer m_GradientDirectionContainer{};
342
344 unsigned int m_NumberOfGradientDirections{};
345
347 unsigned int m_NumberOfBaselineImages{};
348
350 ReferencePixelType m_Threshold{};
351
353 TTensorPixelType m_BValue{};
354
356 GradientImageTypeEnumeration m_GradientImageTypeEnumeration{};
357
359 bool m_MaskImagePresent{};
360};
361} // namespace itk
362
363#ifndef ITK_MANUAL_INSTANTIATION
364# include "itkDiffusionTensor3DReconstructionImageFilter.hxx"
365#endif
366
367#endif
Contains all enum classes used by DiffusionTensor3DReconstructionImageFilter class.
This class takes as input one or more reference image (acquired in the absence of diffusion sensitizi...
void SetGradientImage(GradientDirectionContainerType *, const GradientImagesType *gradientImage)
void AddGradientImage(const GradientDirectionType &, const GradientImageType *gradientImage)
void VerifyPreconditions() const override
Verifies that the process object has been configured correctly, that all required inputs are set,...
void PrintSelf(std::ostream &os, Indent indent) const override
void SetMaskSpatialObject(MaskSpatialObjectType *maskSpatialObject)
virtual GradientDirectionType GetGradientDirection(unsigned int idx) const
void DynamicThreadedGenerateData(const OutputImageRegionType &outputRegionForThread) override
~DiffusionTensor3DReconstructionImageFilter() override=default
void SetMaskImage(MaskImageType *maskImage)
const GradientImageType * GetGradientImage(unsigned int index) const
Represent a diffusion tensor as used in DTI images.
typename OutputImageType::RegionType OutputImageRegionType
Base class for filters that take an image as input and produce an image as output.
Templated n-dimensional image class.
Definition: itkImage.h:89
Control indentation during Print() invocation.
Definition: itkIndent.h:50
Light weight base class for most itk classes.
virtual void SetNthInput(DataObjectPointerArraySizeType idx, DataObject *input)
DataObject * GetInput(const DataObjectIdentifierType &key)
Return an input.
Templated n-dimensional vector image class.
Define a front-end to the STL "vector" container that conforms to the IndexedContainerInterface.
#define itkConceptMacro(name, concept)
The "itk" namespace contains all Insight Segmentation and Registration Toolkit (ITK) classes....
ITKCommon_EXPORT std::ostream & operator<<(std::ostream &out, typename AnatomicalOrientation::CoordinateEnum value)