From bd2c6b9f9fa4b815153b200081de0450429a882e Mon Sep 17 00:00:00 2001 From: malaterre Date: Mon, 31 Jan 2005 05:24:21 +0000 Subject: [PATCH] ENH: Getting toward a nice gdcmDecompressor. Now RLE and JPEG are getting similar in behavior. Also patch vtkgdvmViewer since I couldnt see D_CLUNIE_RG2_RLE.dcm properly... --- src/gdcmJPEGFragmentsInfo.cxx | 6 +- src/gdcmJPEGFragmentsInfo.h | 6 +- src/gdcmPixelReadConvert.cxx | 146 +--------------------------------- src/gdcmPixelReadConvert.h | 11 +-- src/gdcmRLEFrame.h | 8 +- src/gdcmRLEFramesInfo.cxx | 142 ++++++++++++++++++++++++++++++++- src/gdcmRLEFramesInfo.h | 11 ++- vtk/vtkgdcmViewer.cxx | 7 +- 8 files changed, 169 insertions(+), 168 deletions(-) diff --git a/src/gdcmJPEGFragmentsInfo.cxx b/src/gdcmJPEGFragmentsInfo.cxx index b76548b9..6fcd14ef 100644 --- a/src/gdcmJPEGFragmentsInfo.cxx +++ b/src/gdcmJPEGFragmentsInfo.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmJPEGFragmentsInfo.cxx,v $ Language: C++ - Date: $Date: 2005/01/31 04:15:33 $ - Version: $Revision: 1.16 $ + Date: $Date: 2005/01/31 05:24:21 $ + Version: $Revision: 1.17 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -69,7 +69,7 @@ void JPEGFragmentsInfo::Print( std::ostream &os, std::string const &indent ) os << std::endl; } -void JPEGFragmentsInfo::DecompressJPEGFramesFromFile(std::ifstream *fp, uint8_t *buffer, int nBits, int , int ) +void JPEGFragmentsInfo::DecompressFromFile(std::ifstream *fp, uint8_t *buffer, int nBits, int , int ) { // Pointer to the Raw image uint8_t *localRaw = buffer; diff --git a/src/gdcmJPEGFragmentsInfo.h b/src/gdcmJPEGFragmentsInfo.h index 0a09573f..9b4b0fdd 100644 --- a/src/gdcmJPEGFragmentsInfo.h +++ b/src/gdcmJPEGFragmentsInfo.h @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmJPEGFragmentsInfo.h,v $ Language: C++ - Date: $Date: 2005/01/31 04:15:33 $ - Version: $Revision: 1.18 $ + Date: $Date: 2005/01/31 05:24:21 $ + Version: $Revision: 1.19 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -44,7 +44,7 @@ public: ~JPEGFragmentsInfo(); void Print( std::ostream &os = std::cout, std::string const & indent = "" ); - void DecompressJPEGFramesFromFile(std::ifstream *fp, uint8_t *buffer, int nBits, int numBytes, int length); + void DecompressFromFile(std::ifstream *fp, uint8_t *buffer, int nBits, int numBytes, int length); void AddFragment(JPEGFragment *fragment); JPEGFragment *GetFirstFragment(); diff --git a/src/gdcmPixelReadConvert.cxx b/src/gdcmPixelReadConvert.cxx index 65225200..1536ad4a 100644 --- a/src/gdcmPixelReadConvert.cxx +++ b/src/gdcmPixelReadConvert.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.cxx,v $ Language: C++ - Date: $Date: 2005/01/31 04:15:33 $ - Version: $Revision: 1.40 $ + Date: $Date: 2005/01/31 05:24:21 $ + Version: $Revision: 1.41 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -129,144 +129,6 @@ void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp ) } } -/** - * \brief Try to deal with RLE 16 Bits. - * We assume the RLE has already been parsed and loaded in - * Raw (through \ref ReadAndDecompressJPEGFile ). - * We here need to make 16 Bits Pixels from Low Byte and - * High Byte 'Planes'...(for what it may mean) - * @return Boolean - */ -bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames ) -{ - size_t pixelNumber = XSize * YSize; - size_t rawSize = XSize * YSize * NumberOfFrames; - - // We assumed Raw contains the decoded RLE pixels but as - // 8 bits per pixel. In order to convert those pixels to 16 bits - // per pixel we cannot work in place within Raw and hence - // we copy it in a safe place, say copyRaw. - - uint8_t* copyRaw = new uint8_t[rawSize * 2]; - memmove( copyRaw, Raw, rawSize * 2 ); - - uint8_t* x = Raw; - uint8_t* a = copyRaw; - uint8_t* b = a + pixelNumber; - - for ( int i = 0; i < NumberOfFrames; i++ ) - { - for ( unsigned int j = 0; j < pixelNumber; j++ ) - { - *(x++) = *(b++); - *(x++) = *(a++); - } - } - - delete[] copyRaw; - - /// \todo check that operator new []didn't fail, and sometimes return false - return true; -} - -/** - * \brief Implementation of the RLE decoding algorithm for decompressing - * a RLE fragment. [refer to PS 3.5-2003, section G.3.2 p 86] - * @param subRaw Sub region of \ref Raw where the decoded fragment - * should be placed. - * @param fragmentSize The length of the binary fragment as found on the disk. - * @param RawSegmentSize The expected length of the fragment ONCE - * Raw. - * @param fp File Pointer: on entry the position should be the one of - * the fragment to be decoded. - */ -bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t *subRaw, - long fragmentSize, - long RawSegmentSize, - std::ifstream *fp ) -{ - int8_t count; - long numberOfOutputBytes = 0; - long numberOfReadBytes = 0; - - while( numberOfOutputBytes < RawSegmentSize ) - { - fp->read( (char*)&count, 1 ); - numberOfReadBytes += 1; - if ( count >= 0 ) - // Note: count <= 127 comparison is always true due to limited range - // of data type int8_t [since the maximum of an exact width - // signed integer of width N is 2^(N-1) - 1, which for int8_t - // is 127]. - { - fp->read( (char*)subRaw, count + 1); - numberOfReadBytes += count + 1; - subRaw += count + 1; - numberOfOutputBytes += count + 1; - } - else - { - if ( ( count <= -1 ) && ( count >= -127 ) ) - { - int8_t newByte; - fp->read( (char*)&newByte, 1); - numberOfReadBytes += 1; - for( int i = 0; i < -count + 1; i++ ) - { - subRaw[i] = newByte; - } - subRaw += -count + 1; - numberOfOutputBytes += -count + 1; - } - } - // if count = 128 output nothing - - if ( numberOfReadBytes > fragmentSize ) - { - gdcmVerboseMacro( "Read more bytes than the segment size."); - return false; - } - } - return true; -} - -/** - * \brief Reads from disk the Pixel Data of 'Run Length Encoded' - * Dicom encapsulated file and decompress it. - * @param fp already open File Pointer - * at which the pixel data should be copied - * @return Boolean - */ -bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream *fp ) -{ - uint8_t *subRaw = Raw; - long RawSegmentSize = XSize * YSize; - - // Loop on the frame[s] - RLEFrame *frame = RLEInfo->GetFirstFrame(); - while( frame ) - { - // Loop on the fragments - for( unsigned int k = 1; k <= frame->GetNumberOfFragments(); k++ ) - { - fp->seekg(frame->GetOffset(k),std::ios::beg); - ReadAndDecompressRLEFragment(subRaw, - frame->GetLength(k), - RawSegmentSize, - fp); - subRaw += RawSegmentSize; - } - frame = RLEInfo->GetNextFrame(); - } - - if ( BitsAllocated == 16 ) - { - // Try to deal with RLE 16 Bits - (void)DecompressRLE16BitsFromRLE8Bits( ZSize ); - } - - return true; -} /** * \brief Swap the bytes, according to \ref SwapCode. @@ -398,7 +260,7 @@ bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp ) int length = XSize * YSize * SamplesPerPixel; int numberBytes = BitsAllocated / 8; - JPEGInfo->DecompressJPEGFramesFromFile(fp, Raw, BitsStored, numberBytes, length ); + JPEGInfo->DecompressFromFile(fp, Raw, BitsStored, numberBytes, length ); return true; } @@ -578,7 +440,7 @@ bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp ) } else if ( IsRLELossless ) { - if ( ! ReadAndDecompressRLEFile( fp ) ) + if ( ! RLEInfo->ReadAndDecompressRLEFile( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) ) { gdcmVerboseMacro( "RLE decompressor failed." ); return false; diff --git a/src/gdcmPixelReadConvert.h b/src/gdcmPixelReadConvert.h index 047d3193..aea3ec34 100644 --- a/src/gdcmPixelReadConvert.h +++ b/src/gdcmPixelReadConvert.h @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmPixelReadConvert.h,v $ Language: C++ - Date: $Date: 2005/01/31 03:22:26 $ - Version: $Revision: 1.15 $ + Date: $Date: 2005/01/31 05:24:21 $ + Version: $Revision: 1.16 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -60,13 +60,7 @@ public: private: // Use the fp: - bool ReadAndDecompressRLEFragment( - uint8_t *subDecompressed, - long fragmentSize, - long decompressedSegmentSize, - std::ifstream *fp ); void ReadAndDecompress12BitsTo16Bits( std::ifstream *fp ) throw ( FormatError ); - bool ReadAndDecompressRLEFile( std::ifstream *fp ); bool ReadAndDecompressJPEGFile( std::ifstream *fp ); void BuildLUTRGBA( std::ifstream *fp ); @@ -74,7 +68,6 @@ private: // In place (within Decompressed and with no fp access) decompression // or convertion: void BuildLUTRGBA(); - bool DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames ); void ConvertSwapZone(); void ConvertReorderEndianity(); bool ConvertReArrangeBits() throw ( FormatError ); diff --git a/src/gdcmRLEFrame.h b/src/gdcmRLEFrame.h index adac8f92..ac8eac93 100644 --- a/src/gdcmRLEFrame.h +++ b/src/gdcmRLEFrame.h @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmRLEFrame.h,v $ Language: C++ - Date: $Date: 2005/01/26 11:42:02 $ - Version: $Revision: 1.12 $ + Date: $Date: 2005/01/31 05:24:21 $ + Version: $Revision: 1.13 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -50,9 +50,9 @@ public: void SetNumberOfFragments(unsigned int number) { NumberFragments = number; }; unsigned int GetNumberOfFragments() { return NumberFragments; }; - void SetOffset(unsigned int id,long offset); + void SetOffset(unsigned int id, long offset); long GetOffset(unsigned int id); - void SetLength(unsigned int id,long length); + void SetLength(unsigned int id, long length); long GetLength(unsigned int id); private: diff --git a/src/gdcmRLEFramesInfo.cxx b/src/gdcmRLEFramesInfo.cxx index 7fece3c5..6f9aed23 100644 --- a/src/gdcmRLEFramesInfo.cxx +++ b/src/gdcmRLEFramesInfo.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmRLEFramesInfo.cxx,v $ Language: C++ - Date: $Date: 2005/01/31 04:15:33 $ - Version: $Revision: 1.8 $ + Date: $Date: 2005/01/31 05:24:21 $ + Version: $Revision: 1.9 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -78,4 +78,142 @@ RLEFrame *RLEFramesInfo::GetNextFrame() return NULL; } +/** + * \brief Reads from disk the Pixel Data of 'Run Length Encoded' + * Dicom encapsulated file and decompress it. + * @param fp already open File Pointer + * at which the pixel data should be copied + * @return Boolean + */ +bool RLEFramesInfo::ReadAndDecompressRLEFile( std::ifstream *fp , uint8_t *raw, int xSize, int ySize, int zSize, int bitsAllocated ) +{ + uint8_t *subRaw = raw; + long RawSegmentSize = xSize * ySize; + + // Loop on the frame[s] + for(RLEFrameList::iterator it = Frames.begin(); it != Frames.end(); ++it) + { + // Loop on the fragments + for( unsigned int k = 1; k <= (*it)->GetNumberOfFragments(); k++ ) + { + fp->seekg((*it)->GetOffset(k),std::ios::beg); + ReadAndDecompressRLEFragment(subRaw, + (*it)->GetLength(k), + RawSegmentSize, + fp); + subRaw += RawSegmentSize; + } + } + + if ( bitsAllocated == 16 ) + { + // Try to deal with RLE 16 Bits + (void)DecompressRLE16BitsFromRLE8Bits( raw, xSize, ySize, zSize ); + } + + return true; +} + +/** + * \brief Implementation of the RLE decoding algorithm for decompressing + * a RLE fragment. [refer to PS 3.5-2003, section G.3.2 p 86] + * @param subRaw Sub region of \ref Raw where the decoded fragment + * should be placed. + * @param fragmentSize The length of the binary fragment as found on the disk. + * @param RawSegmentSize The expected length of the fragment ONCE + * Raw. + * @param fp File Pointer: on entry the position should be the one of + * the fragment to be decoded. + */ +bool RLEFramesInfo::ReadAndDecompressRLEFragment( uint8_t *subRaw, + long fragmentSize, + long RawSegmentSize, + std::ifstream *fp ) +{ + int8_t count; + long numberOfOutputBytes = 0; + long numberOfReadBytes = 0; + + while( numberOfOutputBytes < RawSegmentSize ) + { + fp->read( (char*)&count, 1 ); + numberOfReadBytes += 1; + if ( count >= 0 ) + // Note: count <= 127 comparison is always true due to limited range + // of data type int8_t [since the maximum of an exact width + // signed integer of width N is 2^(N-1) - 1, which for int8_t + // is 127]. + { + fp->read( (char*)subRaw, count + 1); + numberOfReadBytes += count + 1; + subRaw += count + 1; + numberOfOutputBytes += count + 1; + } + else + { + if ( count <= -1 && count >= -127 ) + { + int8_t newByte; + fp->read( (char*)&newByte, 1); + numberOfReadBytes += 1; + for( int i = 0; i < -count + 1; i++ ) + { + subRaw[i] = newByte; + } + subRaw += -count + 1; + numberOfOutputBytes += -count + 1; + } + } + // if count = 128 output nothing + + if ( numberOfReadBytes > fragmentSize ) + { + gdcmVerboseMacro( "Read more bytes than the segment size."); + return false; + } + } + return true; +} + +/** + * \brief Try to deal with RLE 16 Bits. + * We assume the RLE has already been parsed and loaded in + * Raw (through \ref ReadAndDecompressJPEGFile ). + * We here need to make 16 Bits Pixels from Low Byte and + * High Byte 'Planes'...(for what it may mean) + * @return Boolean + */ +bool RLEFramesInfo::DecompressRLE16BitsFromRLE8Bits( uint8_t* raw, int xSize, int ySize,int numberOfFrames ) +{ + size_t pixelNumber = xSize * ySize; + size_t rawSize = xSize * ySize * numberOfFrames; + + // We assumed Raw contains the decoded RLE pixels but as + // 8 bits per pixel. In order to convert those pixels to 16 bits + // per pixel we cannot work in place within Raw and hence + // we copy it in a safe place, say copyRaw. + + uint8_t* copyRaw = new uint8_t[rawSize * 2]; + memmove( copyRaw, raw, rawSize * 2 ); + + uint8_t* x = raw; + uint8_t* a = copyRaw; + uint8_t* b = a + pixelNumber; + + for ( int i = 0; i < numberOfFrames; i++ ) + { + for ( unsigned int j = 0; j < pixelNumber; j++ ) + { + *(x++) = *(b++); + *(x++) = *(a++); + } + } + + delete[] copyRaw; + + /// \todo check that operator new []didn't fail, and sometimes return false + return true; +} + + } // end namespace gdcm diff --git a/src/gdcmRLEFramesInfo.h b/src/gdcmRLEFramesInfo.h index d5fad91e..27c42287 100644 --- a/src/gdcmRLEFramesInfo.h +++ b/src/gdcmRLEFramesInfo.h @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmRLEFramesInfo.h,v $ Language: C++ - Date: $Date: 2005/01/31 04:15:33 $ - Version: $Revision: 1.15 $ + Date: $Date: 2005/01/31 05:24:22 $ + Version: $Revision: 1.16 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -45,6 +45,13 @@ class GDCM_EXPORT RLEFramesInfo public: ~RLEFramesInfo(); void Print( std::ostream &os = std::cout, std::string indent = "" ); + bool ReadAndDecompressRLEFile( std::ifstream *fp, uint8_t *subRaw, int xSize, int ySize, int zSize, int bitsAllocated ); + bool ReadAndDecompressRLEFragment( + uint8_t *subDecompressed, + long fragmentSize, + long decompressedSegmentSize, + std::ifstream *fp ); + bool DecompressRLE16BitsFromRLE8Bits( uint8_t* subRaw, int xSize, int ySize, int NumberOfFrames ); void AddFrame(RLEFrame *frame); diff --git a/vtk/vtkgdcmViewer.cxx b/vtk/vtkgdcmViewer.cxx index d70d4944..9e1b6a59 100644 --- a/vtk/vtkgdcmViewer.cxx +++ b/vtk/vtkgdcmViewer.cxx @@ -15,7 +15,7 @@ #include #include -#include +#include #include #include #include @@ -60,7 +60,7 @@ public: } } } - vtkImageViewer2 *ImageViewer; + vtkImageViewer *ImageViewer; }; @@ -85,7 +85,7 @@ int main(int argc, char *argv[]) vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New(); - vtkImageViewer2 *viewer = vtkImageViewer2::New(); + vtkImageViewer *viewer = vtkImageViewer::New(); if( reader->GetLookupTable() ) { @@ -117,6 +117,7 @@ int main(int argc, char *argv[]) iren->AddObserver(vtkCommand::CharEvent,obs); obs->Delete(); + //viewer->Render(); iren->Initialize(); iren->Start(); -- 2.48.1