00001 /*========================================================================= 00002 00003 Program: GDCM (Grassroots DICOM). A DICOM library 00004 Module: $URL$ 00005 00006 Copyright (c) 2006-2010 Mathieu Malaterre 00007 All rights reserved. 00008 See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details. 00009 00010 This software is distributed WITHOUT ANY WARRANTY; without even 00011 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 00012 PURPOSE. See the above copyright notice for more information. 00013 00014 =========================================================================*/ 00015 // .NAME vtkGDCMImageReader - read DICOM Image files (Pixel Data) 00016 // .SECTION Description 00017 // vtkGDCMImageReader is a source object that reads some DICOM files 00018 // this reader is single threaded. 00019 // .SECTION Implementation note: when FileLowerLeft is set to on the image is not flipped 00020 // upside down as VTK would expect, use this option only if you know what you are doing. 00021 // .SECTION Implementation note: when reading a series of 2D slices, user is 00022 // expected to provide an ordered list of filenames. No sorting will be applied afterward. 00023 // .SECTION Implementation note: Although 99% of the time the Zspacing as read 00024 // from a tag in a 2D DICOM file should be correct, there has been reports that this 00025 // value can be missing, or incorrect, in which case users are advised to override this 00026 // value using the return value from gdcm::IPPSorter::GetZSpacing() and set it via 00027 // vtkImageChangeInformation on the reader itself. 00028 // .SECTION TODO 00029 // This reader does not handle a series of 3D images, only a single 3D (multi frame) or a 00030 // list of 2D files are supported for now. 00031 // .SECTION TODO 00032 // Did not implement SetFilePattern / SetFilePrefix API, move it to protected section for now. 00033 // .SECTION BUG 00034 // Overlay are assumed to have the same extent as image. Right now if overlay origin is not 00035 // 0,0 the overlay will have an offset... 00036 // Only the very first overlay is loaded at the VTK level, for now (even if there are more than one in the file) 00037 // .SECTION DataOrigin 00038 // When the reader is instanciated with FileLowerLeftOn the DataOrigin and Image Position (Patient) are 00039 // identical. But when FileLowerLeft is Off, we have to reorder the Y-line of the image, and thus the DataOrigin 00040 // is then translated to the other side of the image. 00041 // .SECTION Spacing 00042 // When reading a 3D volume, the spacing along the Z dimension might be negative (so as to respect up-side-down) 00043 // as specified in the Image Orientation (Patient) tag. When Z-spacing is 0, this means the multi-frame object 00044 // contains image which do not represent uniform volume. 00045 // .SECTION Warning 00046 // When using vtkGDCMPolyDataReader in conjonction with vtkGDCMImageReader 00047 // it is *required* that FileLowerLeft is set to ON as coordinate system 00048 // would be inconsistant in between the two data structures. 00049 // .SECTION Color Space mapping: 00050 // * VTK_LUMINANCE <-> MONOCHROME2 00051 // * VTK_LUMINANCE_ALPHA <-> Not supported 00052 // * VTK_RGB <-> RGB 00053 // * VTK_RGBA <-> ARGB (deprecated, DICOM 2008) 00054 // * VTK_INVERSE_LUMINANCE <-> MONOCHROME1 00055 // * VTK_LOOKUP_TABLE <-> PALETTE COLOR 00056 // * VTK_YBR <-> YBR_FULL 00057 // 00058 // For detailed information on color space transformation and true lossless transformation see: 00059 // http://apps.sourceforge.net/mediawiki/gdcm/index.php?title=Color_Space_Transformations 00060 00061 // .SECTION See Also 00062 // vtkMedicalImageReader2 vtkMedicalImageProperties vtkGDCMPolyDataReader vtkGDCMImageWriter 00063 // vtkDICOMImageReader 00064 00065 #ifndef VTKGDCMIMAGEREADER_H 00066 #define VTKGDCMIMAGEREADER_H 00067 00068 #include "vtkMedicalImageReader2.h" 00069 #include "vtkImageData.h" 00070 00071 #if (VTK_MAJOR_VERSION >= 5) || ( VTK_MAJOR_VERSION == 4 && VTK_MINOR_VERSION > 5 ) 00072 #else 00073 class vtkMedicalImageProperties; 00074 #endif 00075 #if ( VTK_MAJOR_VERSION == 5 && VTK_MINOR_VERSION > 0 ) 00076 #else 00077 class vtkStringArray; 00078 #endif 00079 class vtkPolyData; 00080 00081 // vtkSystemIncludes.h defines: 00082 // #define VTK_LUMINANCE 1 00083 // #define VTK_LUMINANCE_ALPHA 2 00084 // #define VTK_RGB 3 00085 // #define VTK_RGBA 4 00086 #ifndef VTK_INVERSE_LUMINANCE 00087 #define VTK_INVERSE_LUMINANCE 5 00088 #endif 00089 #ifndef VTK_LOOKUP_TABLE 00090 #define VTK_LOOKUP_TABLE 6 00091 #endif 00092 #ifndef VTK_YBR 00093 #define VTK_YBR 7 00094 #endif 00095 #ifndef VTK_CMYK 00096 #define VTK_CMYK 8 00097 #endif 00098 00099 //BTX 00100 namespace gdcm { class ImageReader; } 00101 //ETX 00102 class vtkMatrix4x4; 00103 class VTK_EXPORT vtkGDCMImageReader : public vtkMedicalImageReader2 00104 { 00105 public: 00106 static vtkGDCMImageReader *New(); 00107 vtkTypeRevisionMacro(vtkGDCMImageReader,vtkMedicalImageReader2); 00108 virtual void PrintSelf(ostream& os, vtkIndent indent); 00109 00110 // Description: is the given file name a DICOM file containing an image ? 00111 virtual int CanReadFile(const char* fname); 00112 00113 // Description: 00114 // Valid extensions 00115 virtual const char* GetFileExtensions() 00116 { 00117 // I would like to get rid of ACR/NEMA/IMA so only allow dcm extension for now 00118 return ".dcm .DCM"; 00119 } 00120 00121 // Description: 00122 // A descriptive name for this format 00123 virtual const char* GetDescriptiveName() 00124 { 00125 return "DICOM"; 00126 } 00127 00128 // Description: 00129 // Get the Image Position (Patient) as stored in the DICOM file 00130 // This is a read-only data member 00131 vtkGetObjectMacro(DirectionCosines, vtkMatrix4x4); 00132 00133 #if (VTK_MAJOR_VERSION >= 5) || ( VTK_MAJOR_VERSION == 4 && VTK_MINOR_VERSION > 5 ) 00134 #else 00135 // Description: 00136 // Get the medical image properties object 00137 vtkGetObjectMacro(MedicalImageProperties, vtkMedicalImageProperties); 00138 #endif 00139 virtual void SetMedicalImageProperties(vtkMedicalImageProperties *pd); 00140 00141 #if ( VTK_MAJOR_VERSION == 5 && VTK_MINOR_VERSION > 0 ) 00142 #else 00143 virtual void SetFileNames(vtkStringArray*); 00144 vtkGetObjectMacro(FileNames, vtkStringArray); 00145 #endif 00146 00147 // Description: 00148 // Specifically request to load the overlay into the gdcm-VTK layer (gdcm always loads them when found). 00149 // If no overlay is found in the image, then the vtkImageData for the overlay will be empty. 00150 vtkGetMacro(LoadOverlays,int); 00151 vtkSetMacro(LoadOverlays,int); 00152 vtkBooleanMacro(LoadOverlays,int); 00153 00154 // Description: 00155 // Set/Get whether or not to load the Icon as vtkImageData (if found in the DICOM file) 00156 vtkGetMacro(LoadIconImage,int); 00157 vtkSetMacro(LoadIconImage,int); 00158 vtkBooleanMacro(LoadIconImage,int); 00159 00160 // Description: 00161 // Set/Get whether or not the image was compressed using a lossy compression algorithm 00162 vtkGetMacro(LossyFlag,int); 00163 vtkSetMacro(LossyFlag,int); 00164 vtkBooleanMacro(LossyFlag,int); 00165 00166 // Description: 00167 // Read only: number of overlays as found in this image (multiple overlays per slice is allowed) 00168 // Only valid when LoadOverlays is true 00169 vtkGetMacro(NumberOfOverlays,int); 00170 00171 // Description: 00172 // Read only: number of icon image (there can only be zero or one icon per file) 00173 // Only valid when LoadIconImage is true 00174 vtkGetMacro(NumberOfIconImages,int); 00175 00176 // Description: 00177 // Get Overlay/IconImage 00178 // Remember to ALWAYS use those methods in your code, as the internal number for the output port 00179 // is not garantee to remain the same, as features are added to the reader 00180 #if (VTK_MAJOR_VERSION >= 5) || ( VTK_MAJOR_VERSION == 4 && VTK_MINOR_VERSION > 5 ) 00181 //FIXME: Need to get rid of BTX/ETX if only the Python Wrapper of VTK 4.2 would let me 00182 //BTX 00183 vtkAlgorithmOutput* GetOverlayPort(int index); 00184 vtkAlgorithmOutput* GetIconImagePort(); 00185 //ETX 00186 #endif 00187 vtkImageData* GetOverlay(int i); 00188 vtkImageData* GetIconImage(); 00189 00190 // Description: 00191 // Load image with its associated Lookup Table 00192 vtkGetMacro(ApplyLookupTable,int); 00193 vtkSetMacro(ApplyLookupTable,int); 00194 vtkBooleanMacro(ApplyLookupTable,int); 00195 00196 // Description: 00197 // Load image as YBR 00198 vtkGetMacro(ApplyYBRToRGB,int) 00199 vtkSetMacro(ApplyYBRToRGB,int) 00200 vtkBooleanMacro(ApplyYBRToRGB,int); 00201 00202 // Description: 00203 // Return VTK_LUMINANCE, VTK_INVERSE_LUMINANCE, VTK_RGB, VTK_RGBA, VTK_LOOKUP_TABLE, VTK_YBR or VTK_CMYK 00204 // or 0 when ImageFormat is not handled. 00205 // Warning: For color image, PlanarConfiguration need to be taken into account. 00206 vtkGetMacro(ImageFormat,int); 00207 00208 // Description: 00209 // Return the Planar Configuration. This simply means that the internal DICOM image was stored 00210 // using a particular planar configuration (most of the time: 0) 00211 // For monochrome image, PlanarConfiguration is always 0 00212 vtkGetMacro(PlanarConfiguration,int); 00213 00214 // Description: 00215 // Return the 'raw' information stored in the DICOM file: 00216 // In case of a series of multiple files, only the first file is considered. The Image Orientation (Patient) 00217 // is garantee to remain the same, and image Image Position (Patient) in other slice can be computed 00218 // using the ZSpacing (3rd dimension) 00219 // (0020,0032) DS [87.774866\-182.908510\168.629671] # 32, 3 ImagePositionPatient 00220 // (0020,0037) DS [0.001479\0.999989\-0.004376\-0.002039\-0.004372\-0.999988] # 58, 6 ImageOrientationPatient 00221 vtkGetVector3Macro(ImagePositionPatient,double); 00222 vtkGetVector6Macro(ImageOrientationPatient,double); 00223 00224 // Description: 00225 // Set/Get the first Curve Data: 00226 vtkGetObjectMacro(Curve,vtkPolyData); 00227 virtual void SetCurve(vtkPolyData *pd); 00228 00229 // Description: 00230 // \DEPRECATED: 00231 // Modality LUT 00232 // Value returned by GetShift/GetScale might be innacurate since Shift/Scale could be 00233 // varying along the Series read. Therefore user are advices not to use those functions 00234 // anymore 00235 vtkGetMacro(Shift,double); 00236 vtkGetMacro(Scale,double); 00237 00238 protected: 00239 vtkGDCMImageReader(); 00240 ~vtkGDCMImageReader(); 00241 00242 vtkSetVector6Macro(ImageOrientationPatient,double); 00243 00244 //BTX 00245 void FillMedicalImageInformation(const gdcm::ImageReader &reader); 00246 //ETX 00247 int RequestInformationCompat(); 00248 int RequestDataCompat(); 00249 00250 #if (VTK_MAJOR_VERSION >= 5) || ( VTK_MAJOR_VERSION == 4 && VTK_MINOR_VERSION > 5 ) 00251 int ProcessRequest(vtkInformation* request, 00252 vtkInformationVector** inputVector, 00253 vtkInformationVector* outputVector); 00254 int RequestInformation(vtkInformation *request, 00255 vtkInformationVector **inputVector, 00256 vtkInformationVector *outputVector); 00257 int RequestData(vtkInformation *request, 00258 vtkInformationVector **inputVector, 00259 vtkInformationVector *outputVector); 00260 #else /*(VTK_MAJOR_VERSION >= 5) || ( VTK_MAJOR_VERSION == 4 && VTK_MINOR_VERSION > 5 )*/ 00261 void ExecuteInformation(); 00262 void ExecuteData(vtkDataObject *out); 00263 #endif /*(VTK_MAJOR_VERSION >= 5) || ( VTK_MAJOR_VERSION == 4 && VTK_MINOR_VERSION > 5 )*/ 00264 00265 protected: 00266 #if (VTK_MAJOR_VERSION >= 5) || ( VTK_MAJOR_VERSION == 4 && VTK_MINOR_VERSION > 5 ) 00267 #else 00268 // Description: 00269 // Medical Image properties 00270 vtkMedicalImageProperties *MedicalImageProperties; 00271 #endif 00272 #if ( VTK_MAJOR_VERSION == 5 && VTK_MINOR_VERSION > 0 ) 00273 #else 00274 vtkStringArray *FileNames; 00275 #endif 00276 00277 vtkMatrix4x4 *DirectionCosines; 00278 int LoadOverlays; 00279 int NumberOfOverlays; 00280 int LoadIconImage; 00281 int NumberOfIconImages; 00282 int IconImageDataExtent[6]; 00283 double ImagePositionPatient[3]; 00284 double ImageOrientationPatient[6]; 00285 vtkPolyData *Curve; 00286 00287 int ImageFormat; 00288 // the following 3, should remain optional 00289 int ApplyInverseVideo; 00290 int ApplyLookupTable; 00291 int ApplyYBRToRGB; 00292 // I think that planar configuration need to always be applied as far as VTK is concerned 00293 int ApplyPlanarConfiguration; 00294 int ApplyShiftScale; 00295 00296 int LoadSingleFile(const char *filename, char *pointer, unsigned long &outlen); 00297 00298 double Shift; 00299 double Scale; 00300 int IconDataScalarType; 00301 int IconNumberOfScalarComponents; 00302 int PlanarConfiguration; 00303 int LossyFlag; 00304 int ForceRescale; 00305 00306 protected: 00307 // TODO / FIXME 00308 void SetFilePrefix(const char *) {} 00309 vtkGetStringMacro(FilePrefix); 00310 void SetFilePattern(const char *) {} 00311 vtkGetStringMacro(FilePattern); 00312 00313 private: 00314 vtkGDCMImageReader(const vtkGDCMImageReader&); // Not implemented. 00315 void operator=(const vtkGDCMImageReader&); // Not implemented. 00316 }; 00317 #endif 00318