VTK  9.0.1
vtkNIFTIImageReader.h
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1 /*=========================================================================
2 
3  Program: Visualization Toolkit
4  Module: vtkNIFTIImageReader.h
5 
6  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
7  All rights reserved.
8  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
9 
10  This software is distributed WITHOUT ANY WARRANTY; without even
11  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
12  PURPOSE. See the above copyright notice for more information.
13 
14 =========================================================================*/
35 #ifndef vtkNIFTIImageReader_h
36 #define vtkNIFTIImageReader_h
37 
38 #include "vtkIOImageModule.h" // For export macro
39 #include "vtkImageReader2.h"
40 
42 class vtkMatrix4x4;
43 
44 struct nifti_1_header;
45 
46 //----------------------------------------------------------------------------
47 class VTKIOIMAGE_EXPORT vtkNIFTIImageReader : public vtkImageReader2
48 {
49 public:
51 
54  static vtkNIFTIImageReader* New();
57 
61  void PrintSelf(ostream& os, vtkIndent indent) override;
62 
66  const char* GetFileExtensions() override { return ".nii .nii.gz .img .img.gz .hdr .hdr.gz"; }
67 
71  const char* GetDescriptiveName() override { return "NIfTI"; }
72 
76  int CanReadFile(const char* filename) override;
77 
79 
86  vtkGetMacro(TimeAsVector, bool);
87  vtkSetMacro(TimeAsVector, bool);
88  vtkBooleanMacro(TimeAsVector, bool);
90 
94  int GetTimeDimension() { return this->Dim[4]; }
95  double GetTimeSpacing() { return this->PixDim[4]; }
96 
104  double GetRescaleSlope() { return this->RescaleSlope; }
105  double GetRescaleIntercept() { return this->RescaleIntercept; }
106 
108 
115  vtkGetMacro(PlanarRGB, bool);
116  vtkSetMacro(PlanarRGB, bool);
117  vtkBooleanMacro(PlanarRGB, bool);
119 
130  double GetQFac() { return this->QFac; }
131 
144  vtkMatrix4x4* GetQFormMatrix() { return this->QFormMatrix; }
145 
160  vtkMatrix4x4* GetSFormMatrix() { return this->SFormMatrix; }
161 
165  vtkNIFTIImageHeader* GetNIFTIHeader();
166 
167 protected:
169  ~vtkNIFTIImageReader() override;
170 
174  int RequestInformation(vtkInformation* request, vtkInformationVector** inputVector,
175  vtkInformationVector* outputVector) override;
176 
180  int RequestData(vtkInformation* request, vtkInformationVector** inputVector,
181  vtkInformationVector* outputVector) override;
182 
188  static bool CheckExtension(const char* fname, const char* ext);
189 
198  static char* ReplaceExtension(const char* fname, const char* ext1, const char* ext2);
199 
203  static int CheckNIFTIVersion(const nifti_1_header* hdr);
204 
208  static bool CheckAnalyzeHeader(const nifti_1_header* hdr);
209 
214 
216 
220  double RescaleSlope;
222 
226  double QFac;
227 
229 
235 
239  int Dim[8];
240 
244  double PixDim[8];
245 
250 
254  bool PlanarRGB;
255 
256 private:
257  vtkNIFTIImageReader(const vtkNIFTIImageReader&) = delete;
258  void operator=(const vtkNIFTIImageReader&) = delete;
259 };
260 
261 #endif // vtkNIFTIImageReader_h
vtkImageAlgorithm::RequestData
virtual int RequestData(vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector)
This is called in response to a REQUEST_DATA request from the executive.
vtkImageReader2::PrintSelf
void PrintSelf(ostream &os, vtkIndent indent) override
Methods invoked by print to print information about the object including superclasses.
vtkNIFTIImageReader::GetDescriptiveName
const char * GetDescriptiveName() override
Return a descriptive name that might be useful in a GUI.
Definition: vtkNIFTIImageReader.h:71
vtkNIFTIImageReader::GetTimeDimension
int GetTimeDimension()
Get the time dimension that was stored in the NIFTI header.
Definition: vtkNIFTIImageReader.h:94
vtkInformationVector
Store zero or more vtkInformation instances.
Definition: vtkInformationVector.h:35
vtkNIFTIImageReader::GetSFormMatrix
vtkMatrix4x4 * GetSFormMatrix()
Get a matrix that gives the "sform" orientation and offset for the data.
Definition: vtkNIFTIImageReader.h:160
vtkNIFTIImageReader::RescaleSlope
double RescaleSlope
Definition: vtkNIFTIImageReader.h:220
vtkImageReader2::RequestInformation
int RequestInformation(vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector) override
Subclasses can reimplement this method to collect information from their inputs and set information f...
vtkNIFTIImageReader::QFormMatrix
vtkMatrix4x4 * QFormMatrix
The orientation matrices for the NIFTI file.
Definition: vtkNIFTIImageReader.h:232
vtkNIFTIImageReader::NIFTIHeader
vtkNIFTIImageHeader * NIFTIHeader
A copy of the header from the file that was most recently read.
Definition: vtkNIFTIImageReader.h:249
vtkNIFTIImageReader::GetTimeSpacing
double GetTimeSpacing()
Definition: vtkNIFTIImageReader.h:95
vtkNIFTIImageHeader
Store NIfTI header information.
Definition: vtkNIFTIImageHeader.h:46
vtkNIFTIImageReader::GetQFormMatrix
vtkMatrix4x4 * GetQFormMatrix()
Get a matrix that gives the "qform" orientation and offset for the data.
Definition: vtkNIFTIImageReader.h:144
vtkNIFTIImageReader
Read NIfTI-1 and NIfTI-2 medical image files.
Definition: vtkNIFTIImageReader.h:47
vtkImageReader2::New
static vtkImageReader2 * New()
vtkNIFTIImageReader::GetRescaleSlope
double GetRescaleSlope()
Get the slope and intercept for rescaling the scalar values.
Definition: vtkNIFTIImageReader.h:104
vtkNIFTIImageReader::QFac
double QFac
Is -1 if VTK slice order is opposite to NIFTI slice order, +1 otherwise.
Definition: vtkNIFTIImageReader.h:226
vtkNIFTIImageReader::PlanarRGB
bool PlanarRGB
Use planar RGB instead of the default (packed).
Definition: vtkNIFTIImageReader.h:254
vtkIndent
a simple class to control print indentation
Definition: vtkIndent.h:33
vtkMatrix4x4
represent and manipulate 4x4 transformation matrices
Definition: vtkMatrix4x4.h:35
vtkImageReader2
Superclass of binary file readers.
Definition: vtkImageReader2.h:52
vtkNIFTIImageReader::TimeAsVector
bool TimeAsVector
Read the time dimension as if it was a vector dimension.
Definition: vtkNIFTIImageReader.h:213
nifti_1_header
Data structure defining the fields in the nifti1 header. This binary header should be found at the be...
Definition: vtkNIFTIImagePrivate.h:37
vtkInformation
Store vtkAlgorithm input/output information.
Definition: vtkInformation.h:73
vtkNIFTIImageReader::RescaleIntercept
double RescaleIntercept
Information for rescaling data to quantitative units.
Definition: vtkNIFTIImageReader.h:219
vtkNIFTIImageReader::GetRescaleIntercept
double GetRescaleIntercept()
Definition: vtkNIFTIImageReader.h:105
vtkNIFTIImageReader::SFormMatrix
vtkMatrix4x4 * SFormMatrix
Definition: vtkNIFTIImageReader.h:233
vtkNIFTIImageReader::GetQFac
double GetQFac()
QFac gives the slice order in the NIFTI file versus the VTK image.
Definition: vtkNIFTIImageReader.h:130
vtkImageReader2::CanReadFile
virtual int CanReadFile(const char *vtkNotUsed(fname))
Return non zero if the reader can read the given file name.
Definition: vtkImageReader2.h:283
vtkImageReader2.h
vtkNIFTIImageReader::GetFileExtensions
const char * GetFileExtensions() override
Valid extensions for this file type.
Definition: vtkNIFTIImageReader.h:66