1 /*========================================================================= 2 3 Program: Visualization Toolkit 4 Module: vtkMINCImageReader.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 =========================================================================*/ 15 /*========================================================================= 16 17 Copyright (c) 2006 Atamai, Inc. 18 19 Use, modification and redistribution of the software, in source or 20 binary forms, are permitted provided that the following terms and 21 conditions are met: 22 23 1) Redistribution of the source code, in verbatim or modified 24 form, must retain the above copyright notice, this license, 25 the following disclaimer, and any notices that refer to this 26 license and/or the following disclaimer. 27 28 2) Redistribution in binary form must include the above copyright 29 notice, a copy of this license and the following disclaimer 30 in the documentation or with other materials provided with the 31 distribution. 32 33 3) Modified copies of the source code must be clearly marked as such, 34 and must not be misrepresented as verbatim copies of the source code. 35 36 THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE SOFTWARE "AS IS" 37 WITHOUT EXPRESSED OR IMPLIED WARRANTY INCLUDING, BUT NOT LIMITED TO, 38 THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 39 PURPOSE. IN NO EVENT SHALL ANY COPYRIGHT HOLDER OR OTHER PARTY WHO MAY 40 MODIFY AND/OR REDISTRIBUTE THE SOFTWARE UNDER THE TERMS OF THIS LICENSE 41 BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL OR CONSEQUENTIAL DAMAGES 42 (INCLUDING, BUT NOT LIMITED TO, LOSS OF DATA OR DATA BECOMING INACCURATE 43 OR LOSS OF PROFIT OR BUSINESS INTERRUPTION) ARISING IN ANY WAY OUT OF 44 THE USE OR INABILITY TO USE THE SOFTWARE, EVEN IF ADVISED OF THE 45 POSSIBILITY OF SUCH DAMAGES. 46 47 =========================================================================*/ 48 // .NAME vtkMINCImageReader - A reader for MINC files. 49 // .SECTION Description 50 // MINC is a NetCDF-based medical image file format that was developed 51 // at the Montreal Neurological Institute in 1992. 52 // This class will read a MINC file into VTK, rearranging the data to 53 // match the VTK x, y, and z dimensions, and optionally rescaling 54 // real-valued data to VTK_FLOAT if RescaleRealValuesOn() is set. 55 // If RescaleRealValues is off, then the data will be stored in its 56 // original data type and the GetRescaleSlope(), GetRescaleIntercept() 57 // method can be used to retrieve global rescaling parameters. 58 // If the original file had a time dimension, the SetTimeStep() method 59 // can be used to specify a time step to read. 60 // All of the original header information can be accessed though the 61 // GetImageAttributes() method. 62 // .SECTION See Also 63 // vtkMINCImageWriter vtkMINCImageAttributes 64 // .SECTION Thanks 65 // Thanks to David Gobbi for writing this class and Atamai Inc. for 66 // contributing it to VTK. 67 68 #ifndef vtkMINCImageReader_h 69 #define vtkMINCImageReader_h 70 71 #include "vtkIOMINCModule.h" // For export macro 72 #include "vtkImageReader2.h" 73 74 class vtkStringArray; 75 class vtkIdTypeArray; 76 class vtkDoubleArray; 77 class vtkMatrix4x4; 78 79 // A special class that holds the attributes 80 class vtkMINCImageAttributes; 81 82 class VTKIOMINC_EXPORT vtkMINCImageReader : public vtkImageReader2 83 { 84 public: 85 vtkTypeMacro(vtkMINCImageReader,vtkImageReader2); 86 87 static vtkMINCImageReader *New(); 88 virtual void PrintSelf(ostream& os, vtkIndent indent); 89 90 // Description: 91 // Set the file name. 92 virtual void SetFileName(const char *name); 93 94 // Description: 95 // Get the entension for this file format. GetFileExtensions()96 virtual const char* GetFileExtensions() { 97 return ".mnc"; } 98 99 // Description: 100 // Get the name of this file format. GetDescriptiveName()101 virtual const char* GetDescriptiveName() { 102 return "MINC"; } 103 104 // Description: 105 // Test whether the specified file can be read. 106 virtual int CanReadFile(const char* name); 107 108 // Description: 109 // Get a matrix that describes the orientation of the data. 110 // The three columns of the matrix are the direction cosines 111 // for the x, y and z dimensions respectively. 112 virtual vtkMatrix4x4 *GetDirectionCosines(); 113 114 // Description: 115 // Get the slope and intercept for rescaling the scalar values 116 // to real data values. To convert scalar values to real values, 117 // use the equation y = x*RescaleSlope + RescaleIntercept. 118 virtual double GetRescaleSlope(); 119 virtual double GetRescaleIntercept(); 120 121 // Description: 122 // Rescale real data values to float. If this is done, the 123 // RescaleSlope and RescaleIntercept will be set to 1 and 0 124 // respectively. This is off by default. 125 vtkSetMacro(RescaleRealValues, int); 126 vtkBooleanMacro(RescaleRealValues, int); 127 vtkGetMacro(RescaleRealValues, int); 128 129 // Description: 130 // Get the scalar range of the output from the information in 131 // the file header. This is more efficient that computing the 132 // scalar range, but in some cases the MINC file stores an 133 // incorrect valid_range and the DataRange will be incorrect. 134 virtual double *GetDataRange(); GetDataRange(double range[2])135 virtual void GetDataRange(double range[2]) { 136 double *r = this->GetDataRange(); 137 range[0] = r[0]; range[1] = r[1]; }; 138 139 // Description: 140 // Get the number of time steps in the file. 141 virtual int GetNumberOfTimeSteps(); 142 143 // Description: 144 // Set the time step to read. 145 vtkSetMacro(TimeStep, int); 146 vtkGetMacro(TimeStep, int); 147 148 // Description: 149 // Get the image attributes, which contain patient information and 150 // other useful metadata. 151 virtual vtkMINCImageAttributes *GetImageAttributes(); 152 153 protected: 154 vtkMINCImageReader(); 155 ~vtkMINCImageReader(); 156 157 int MINCImageType; 158 int MINCImageTypeSigned; 159 160 double ValidRange[2]; 161 double ImageRange[2]; 162 double DataRange[2]; 163 164 int NumberOfTimeSteps; 165 int TimeStep; 166 vtkMatrix4x4 *DirectionCosines; 167 double RescaleSlope; 168 double RescaleIntercept; 169 int RescaleRealValues; 170 vtkMINCImageAttributes *ImageAttributes; 171 172 int FileNameHasChanged; 173 174 virtual int OpenNetCDFFile(const char *filename, int& ncid); 175 virtual int CloseNetCDFFile(int ncid); 176 virtual int IndexFromDimensionName(const char *dimName); 177 virtual int ReadMINCFileAttributes(); 178 virtual void FindRangeAndRescaleValues(); 179 static int ConvertMINCTypeToVTKType(int minctype, int mincsigned); 180 181 virtual void ExecuteInformation(); 182 virtual void ExecuteDataWithInformation(vtkDataObject *out, vtkInformation *outInfo); 183 184 private: 185 vtkMINCImageReader(const vtkMINCImageReader&); // Not implemented 186 void operator=(const vtkMINCImageReader&); // Not implemented 187 188 }; 189 190 #endif 191