Medical Imaging Interaction Toolkit  2016.11.0
Medical Imaging Interaction Toolkit
mitkNrrdQBallImageReader.cpp
Go to the documentation of this file.
1 /*===================================================================
2 
3 The Medical Imaging Interaction Toolkit (MITK)
4 
5 Copyright (c) German Cancer Research Center,
6 Division of Medical and Biological Informatics.
7 All rights reserved.
8 
9 This software is distributed WITHOUT ANY WARRANTY; without
10 even the implied warranty of MERCHANTABILITY or FITNESS FOR
11 A PARTICULAR PURPOSE.
12 
13 See LICENSE.txt or http://www.mitk.org for details.
14 
15 ===================================================================*/
16 
18 #include <mitkCustomMimeType.h>
20 
21 #include "itkImageFileReader.h"
22 #include "itkImageRegionIterator.h"
23 #include "itkMetaDataObject.h"
24 #include "itkNrrdImageIO.h"
25 #include "mitkITKImageImport.h"
26 #include "mitkImageDataItem.h"
27 #include <mitkLocaleSwitch.h>
28 
29 namespace mitk
30 {
32  : mitk::AbstractFileReader(other)
33  {
34  }
35 
37  : mitk::AbstractFileReader( CustomMimeType( mitk::DiffusionCoreIOMimeTypes::QBI_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::QBI_MIMETYPE_DESCRIPTION() )
38  {
39  m_ServiceReg = this->RegisterService();
40  }
41 
43  {
44  }
45 
46  std::vector<itk::SmartPointer<BaseData> > NrrdQBallImageReader::Read()
47  {
48  std::vector<itk::SmartPointer<mitk::BaseData> > result;
49  std::string location = GetInputLocation();
50 
51  if ( location == "")
52  {
53  throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename of the vessel tree to be read is empty!");
54  }
55  else
56  {
57  try
58  {
59  mitk::LocaleSwitch localeSwitch("C");
60 
61  typedef itk::VectorImage<float,3> ImageType;
63  typedef itk::ImageFileReader<ImageType> FileReaderType;
65  reader->SetImageIO(io);
66  reader->SetFileName(location);
67  reader->Update();
68  ImageType::Pointer img = reader->GetOutput();
69 
70  typedef itk::Image<itk::Vector<float,QBALL_ODFSIZE>,3> VecImgType;
72  vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
73  vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
74  vecImg->SetDirection( img->GetDirection() ); // Set the image direction
75  vecImg->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
76  vecImg->SetBufferedRegion( img->GetLargestPossibleRegion() );
77  vecImg->Allocate();
78 
79  itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
80  ot.GoToBegin();
81 
82  itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
83 
84  typedef ImageType::PixelType VarPixType;
85  typedef VecImgType::PixelType FixPixType;
86 
87  for (it.GoToBegin(); !it.IsAtEnd(); ++it)
88  {
89  VarPixType vec = it.Get();
90  FixPixType fixVec(vec.GetDataPointer());
91  ot.Set(fixVec);
92  ++ot;
93  }
94 
95  OutputType::Pointer resultImage = OutputType::New();
96  resultImage->InitializeByItk( vecImg.GetPointer() );
97  resultImage->SetVolume( vecImg->GetBufferPointer() );
98  result.push_back( resultImage.GetPointer() );
99 
100  }
101  catch(std::exception& e)
102  {
103  throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
104  }
105  catch(...)
106  {
107  throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!");
108  }
109  }
110  return result;
111  }
112 
113 } //namespace MITK
114 
115 mitk::NrrdQBallImageReader* mitk::NrrdQBallImageReader::Clone() const
116 {
117  return new NrrdQBallImageReader(*this);
118 }
itk::SmartPointer< Self > Pointer
DataCollection - Class to facilitate loading/accessing structured data.
The CustomMimeType class represents a custom mime-type which may be registered as a service object...
static Pointer New()
map::core::discrete::Elements< 3 >::InternalImageType ImageType
us::ServiceRegistration< IFileReader > RegisterService(us::ModuleContext *context=us::GetModuleContext())
Convenience class to temporarily change the current locale.
virtual std::vector< itk::SmartPointer< BaseData > > Read() override
Reads a path or stream and creates a list of BaseData objects.
Base class for creating mitk::BaseData objects from files or streams.
unsigned short PixelType
virtual std::string GetInputLocation() const override
Get the current input location.
static itkEventMacro(BoundingShapeInteractionEvent, itk::AnyEvent) class MITKBOUNDINGSHAPE_EXPORT BoundingShapeInteractor Pointer New()
Basic interaction methods for mitk::GeometryData.