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213 lines
6.7 KiB
C++
213 lines
6.7 KiB
C++
/*=========================================================================
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Program: Visualization Toolkit
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Module: vtkMINCImageReader.h
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Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
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All rights reserved.
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See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
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This software is distributed WITHOUT ANY WARRANTY; without even
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the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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PURPOSE. See the above copyright notice for more information.
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=========================================================================*/
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/*=========================================================================
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Copyright (c) 2006 Atamai, Inc.
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Use, modification and redistribution of the software, in source or
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binary forms, are permitted provided that the following terms and
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conditions are met:
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1) Redistribution of the source code, in verbatim or modified
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form, must retain the above copyright notice, this license,
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the following disclaimer, and any notices that refer to this
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license and/or the following disclaimer.
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2) Redistribution in binary form must include the above copyright
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notice, a copy of this license and the following disclaimer
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in the documentation or with other materials provided with the
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distribution.
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3) Modified copies of the source code must be clearly marked as such,
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and must not be misrepresented as verbatim copies of the source code.
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THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE SOFTWARE "AS IS"
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WITHOUT EXPRESSED OR IMPLIED WARRANTY INCLUDING, BUT NOT LIMITED TO,
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THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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PURPOSE. IN NO EVENT SHALL ANY COPYRIGHT HOLDER OR OTHER PARTY WHO MAY
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MODIFY AND/OR REDISTRIBUTE THE SOFTWARE UNDER THE TERMS OF THIS LICENSE
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BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL OR CONSEQUENTIAL DAMAGES
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(INCLUDING, BUT NOT LIMITED TO, LOSS OF DATA OR DATA BECOMING INACCURATE
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OR LOSS OF PROFIT OR BUSINESS INTERRUPTION) ARISING IN ANY WAY OUT OF
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THE USE OR INABILITY TO USE THE SOFTWARE, EVEN IF ADVISED OF THE
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POSSIBILITY OF SUCH DAMAGES.
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=========================================================================*/
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/**
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* @class vtkMINCImageReader
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* @brief A reader for MINC files.
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*
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* MINC is a NetCDF-based medical image file format that was developed
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* at the Montreal Neurological Institute in 1992.
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* This class will read a MINC file into VTK, rearranging the data to
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* match the VTK x, y, and z dimensions, and optionally rescaling
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* real-valued data to VTK_FLOAT if RescaleRealValuesOn() is set.
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* If RescaleRealValues is off, then the data will be stored in its
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* original data type and the GetRescaleSlope(), GetRescaleIntercept()
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* method can be used to retrieve global rescaling parameters.
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* If the original file had a time dimension, the SetTimeStep() method
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* can be used to specify a time step to read.
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* All of the original header information can be accessed though the
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* GetImageAttributes() method.
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* @sa
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* vtkMINCImageWriter vtkMINCImageAttributes
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* @par Thanks:
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* Thanks to David Gobbi for writing this class and Atamai Inc. for
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* contributing it to VTK.
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*/
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#ifndef vtkMINCImageReader_h
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#define vtkMINCImageReader_h
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#include "vtkIOMINCModule.h" // For export macro
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#include "vtkImageReader2.h"
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class vtkStringArray;
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class vtkIdTypeArray;
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class vtkDoubleArray;
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class vtkMatrix4x4;
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// A special class that holds the attributes
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class vtkMINCImageAttributes;
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class VTKIOMINC_EXPORT vtkMINCImageReader : public vtkImageReader2
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{
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public:
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vtkTypeMacro(vtkMINCImageReader, vtkImageReader2);
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static vtkMINCImageReader* New();
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void PrintSelf(ostream& os, vtkIndent indent) override;
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/**
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* Set the file name.
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*/
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void SetFileName(const char* name) override;
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/**
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* Get the extension for this file format.
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*/
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const char* GetFileExtensions() override { return ".mnc"; }
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/**
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* Get the name of this file format.
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*/
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const char* GetDescriptiveName() override { return "MINC"; }
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/**
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* Test whether the specified file can be read.
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*/
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int CanReadFile(const char* name) override;
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/**
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* Get a matrix that describes the orientation of the data.
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* The three columns of the matrix are the direction cosines
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* for the x, y and z dimensions respectively.
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*/
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virtual vtkMatrix4x4* GetDirectionCosines();
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//@{
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/**
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* Get the slope and intercept for rescaling the scalar values
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* to real data values. To convert scalar values to real values,
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* use the equation y = x*RescaleSlope + RescaleIntercept.
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*/
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virtual double GetRescaleSlope();
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virtual double GetRescaleIntercept();
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//@}
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//@{
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/**
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* Rescale real data values to float. If this is done, the
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* RescaleSlope and RescaleIntercept will be set to 1 and 0
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* respectively. This is off by default.
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*/
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vtkSetMacro(RescaleRealValues, vtkTypeBool);
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vtkBooleanMacro(RescaleRealValues, vtkTypeBool);
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vtkGetMacro(RescaleRealValues, vtkTypeBool);
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//@}
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//@{
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/**
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* Get the scalar range of the output from the information in
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* the file header. This is more efficient that computing the
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* scalar range, but in some cases the MINC file stores an
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* incorrect valid_range and the DataRange will be incorrect.
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*/
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virtual double* GetDataRange() VTK_SIZEHINT(2);
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virtual void GetDataRange(double range[2])
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{
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double* r = this->GetDataRange();
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range[0] = r[0];
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range[1] = r[1];
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}
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//@}
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/**
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* Get the number of time steps in the file.
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*/
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virtual int GetNumberOfTimeSteps();
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//@{
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/**
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* Set the time step to read.
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*/
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vtkSetMacro(TimeStep, int);
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vtkGetMacro(TimeStep, int);
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//@}
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/**
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* Get the image attributes, which contain patient information and
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* other useful metadata.
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*/
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virtual vtkMINCImageAttributes* GetImageAttributes();
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protected:
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vtkMINCImageReader();
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~vtkMINCImageReader() override;
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int MINCImageType;
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int MINCImageTypeSigned;
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double ValidRange[2];
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double ImageRange[2];
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double DataRange[2];
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int NumberOfTimeSteps;
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int TimeStep;
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vtkMatrix4x4* DirectionCosines;
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double RescaleSlope;
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double RescaleIntercept;
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vtkTypeBool RescaleRealValues;
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vtkMINCImageAttributes* ImageAttributes;
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int FileNameHasChanged;
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virtual int OpenNetCDFFile(const char* filename, int& ncid);
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virtual int CloseNetCDFFile(int ncid);
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virtual int IndexFromDimensionName(const char* dimName);
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virtual int ReadMINCFileAttributes();
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virtual void FindRangeAndRescaleValues();
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static int ConvertMINCTypeToVTKType(int minctype, int mincsigned);
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void ExecuteInformation() override;
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void ExecuteDataWithInformation(vtkDataObject* out, vtkInformation* outInfo) override;
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private:
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vtkMINCImageReader(const vtkMINCImageReader&) = delete;
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void operator=(const vtkMINCImageReader&) = delete;
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};
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#endif
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