1 /*=========================================================================
4 Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
6 Date: $Date: 2007/09/04 13:42:57 $
7 Version: $Revision: 1.120 $
9 Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
10 l'Image). All rights reserved. See Doc/License.txt or
11 http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
13 This software is distributed WITHOUT ANY WARRANTY; without even
14 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 PURPOSE. See the above copyright notices for more information.
17 =========================================================================*/
19 #include "gdcmPixelReadConvert.h"
20 #include "gdcmDebug.h"
22 #include "gdcmGlobal.h"
24 #include "gdcmDocEntry.h"
25 #include "gdcmRLEFramesInfo.h"
26 #include "gdcmJPEGFragmentsInfo.h"
29 #include <stdio.h> //for sscanf
31 #if defined(__BORLANDC__)
32 #include <mem.h> // for memset
35 namespace GDCM_NAME_SPACE
38 //bool ReadMPEGFile (std::ifstream *fp, char *inputdata, size_t lenght);
39 bool gdcm_read_JPEG2000_file (void* raw,
40 char *inputdata, size_t inputlength);
41 //-----------------------------------------------------------------------------
42 #define str2num(str, typeNum) *((typeNum *)(str))
44 //-----------------------------------------------------------------------------
45 // Constructor / Destructor
47 PixelReadConvert::PixelReadConvert()
63 /// Canonical Destructor
64 PixelReadConvert::~PixelReadConvert()
69 //-----------------------------------------------------------------------------
72 * \brief Predicate to know whether the image[s] (once Raw) is RGB.
73 * \note See comments of \ref ConvertHandleColor
75 bool PixelReadConvert::IsRawRGB()
78 || PlanarConfiguration == 2
86 * \brief Gets various usefull informations from the file header
87 * @param file gdcm::File pointer
88 * @param fileHelper gdcm::FileHelper pointer
90 void PixelReadConvert::GrabInformationsFromFile( File *file,
91 FileHelper *fileHelper )
93 // Number of Bits Allocated for storing a Pixel is defaulted to 16
94 // when absent from the file.
95 BitsAllocated = file->GetBitsAllocated();
96 if ( BitsAllocated == 0 )
101 else if (BitsAllocated > 8 && BitsAllocated < 16 && BitsAllocated != 12)
105 // Number of "Bits Stored", defaulted to number of "Bits Allocated"
106 // when absent from the file.
107 BitsStored = file->GetBitsStored();
108 if ( BitsStored == 0 )
110 BitsStored = BitsAllocated;
113 // High Bit Position, defaulted to "Bits Allocated" - 1
114 HighBitPosition = file->GetHighBitPosition();
115 if ( HighBitPosition == 0 )
117 HighBitPosition = BitsAllocated - 1;
120 XSize = file->GetXSize();
121 YSize = file->GetYSize();
122 ZSize = file->GetZSize();
123 TSize = file->GetTSize();
124 SamplesPerPixel = file->GetSamplesPerPixel();
125 //PixelSize = file->GetPixelSize(); Useless
126 PixelSign = file->IsSignedPixelData();
127 SwapCode = file->GetSwapCode();
129 IsPrivateGETransferSyntax = IsMPEG
130 = IsJPEG2000 = IsJPEGLS = IsJPEGLossy
131 = IsJPEGLossless = IsRLELossless
134 if (! file->IsDicomV3() ) // Should be ACR-NEMA file
140 std::string ts = file->GetTransferSyntax();
143 while (true) // shorter to write than 'if elseif elseif elseif' ...
145 // mind the order : check the most usual first.
146 if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRLittleEndian) break;
147 if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian ) break;
148 if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian) break;
149 if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRBigEndianPrivateGE) break;
150 // DeflatedExplicitVRLittleEndian syntax means the whole Dataset (Header + Pixels) is compressed !
151 // Not dealt with ! (Parser hangs)
152 //if( IsRaw = Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::DeflatedExplicitVRLittleEndian) break;
155 // cache whether this is a strange GE transfer syntax (which uses
156 // a little endian transfer syntax for the header and a big endian
157 // transfer syntax for the pixel data).
158 IsPrivateGETransferSyntax =
159 ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRBigEndianPrivateGE );
161 IsMPEG = IsJPEG2000 = IsJPEGLS = IsJPEGLossy = IsJPEGLossless = IsRLELossless = false;
166 // mind the order : check the most usual first.
167 if( IsJPEGLossy = Global::GetTS()->IsJPEGLossy(ts) ) break;
168 if( IsJPEGLossless = Global::GetTS()->IsJPEGLossless(ts) ) break;
169 if( IsRLELossless = Global::GetTS()->IsRLELossless(ts) ) break;
170 if( IsJPEG2000 = Global::GetTS()->IsJPEG2000(ts) ) break;
171 if( IsMPEG = Global::GetTS()->IsMPEG(ts) ) break;
172 if( IsJPEGLS = Global::GetTS()->IsJPEGLS(ts) ) break;
173 // DeflatedExplicitVRLittleEndian is considered as 'Unexpected' (we don't know yet how to process !)
174 gdcmWarningMacro("Unexpected Transfer Syntax :[" << ts << "]");
180 PixelOffset = file->GetPixelOffset();
181 PixelDataLength = file->GetPixelAreaLength();
182 RLEInfo = file->GetRLEInfo();
183 JPEGInfo = file->GetJPEGInfo();
185 IsMonochrome = file->IsMonochrome();
186 IsMonochrome1 = file->IsMonochrome1();
187 IsPaletteColor = file->IsPaletteColor();
188 IsYBRFull = file->IsYBRFull();
190 PlanarConfiguration = file->GetPlanarConfiguration();
192 /////////////////////////////////////////////////////////////////
194 HasLUT = file->HasLUT();
197 // Just in case some access to a File element requires disk access.
198 LutRedDescriptor = file->GetEntryString( 0x0028, 0x1101 );
199 LutGreenDescriptor = file->GetEntryString( 0x0028, 0x1102 );
200 LutBlueDescriptor = file->GetEntryString( 0x0028, 0x1103 );
202 // FIXME : The following comment is probabely meaningless, since LUT are *always*
203 // loaded at parsing time, whatever their length is.
205 // Depending on the value of Document::MAX_SIZE_LOAD_ELEMENT_VALUE
206 // [ refer to invocation of Document::SetMaxSizeLoadEntry() in
207 // Document::Document() ], the loading of the value (content) of a
208 // [Bin|Val]Entry occurence migth have been hindered (read simply NOT
209 // loaded). Hence, we first try to obtain the LUTs data from the file
210 // and when this fails we read the LUTs data directly from disk.
211 // \TODO Reading a [Bin|Val]Entry directly from disk is a kludge.
212 // We should NOT bypass the [Bin|Val]Entry class. Instead
213 // an access to an UNLOADED content of a [Bin|Val]Entry occurence
214 // (e.g. DataEntry::GetBinArea()) should force disk access from
215 // within the [Bin|Val]Entry class itself. The only problem
216 // is that the [Bin|Val]Entry is unaware of the FILE* is was
217 // parsed from. Fix that. FIXME.
220 file->LoadEntryBinArea(0x0028, 0x1201);
221 LutRedData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1201 );
224 gdcmWarningMacro("Unable to read Red Palette Color Lookup Table data");
228 file->LoadEntryBinArea(0x0028, 0x1202);
229 LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 );
232 gdcmWarningMacro("Unable to read Green Palette Color Lookup Table data");
236 file->LoadEntryBinArea(0x0028, 0x1203);
237 LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 );
240 gdcmWarningMacro("Unable to read Blue Palette Color Lookup Table data");
245 ComputeRawAndRGBSizes();
248 /// \brief Reads from disk and decompresses Pixels
249 bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp )
251 // ComputeRawAndRGBSizes is already made by
252 // ::GrabInformationsFromfile. So, the structure sizes are
256 //////////////////////////////////////////////////
257 //// First stage: get our hands on the Pixel Data.
260 gdcmWarningMacro( "Unavailable file pointer." );
264 fp->seekg( PixelOffset, std::ios::beg );
265 if ( fp->fail() || fp->eof() )
267 gdcmWarningMacro( "Unable to find PixelOffset in file." );
273 //////////////////////////////////////////////////
275 CallStartMethod(); // for progress bar
276 unsigned int count = 0;
277 unsigned int frameSize;
278 unsigned int bitsAllocated = BitsAllocated;
279 //if(bitsAllocated == 12)
280 if(bitsAllocated > 8 && bitsAllocated < 16)
282 frameSize = XSize*YSize*SamplesPerPixel*bitsAllocated/8;
284 //// Second stage: read from disk and decompress.
286 if ( BitsAllocated == 12 ) // We suppose 'BitsAllocated' = 12 only exist for uncompressed files
288 ReadAndDecompress12BitsTo16Bits( fp);
292 // This problem can be found when some obvious informations are found
293 // after the field containing the image data. In this case, these
294 // bad data are added to the size of the image (in the PixelDataLength
295 // variable). But RawSize is the right size of the image !
296 if ( PixelDataLength != RawSize )
298 gdcmWarningMacro( "Mismatch between PixelReadConvert : "
299 << PixelDataLength << " and RawSize : " << RawSize );
302 //todo : is it the right patch?
303 char *raw = (char*)Raw;
304 uint32_t remainingLength;
306 unsigned int lengthToRead;
308 if ( PixelDataLength > RawSize )
309 lengthToRead = RawSize;
311 lengthToRead = PixelDataLength;
313 // perform a frame by frame reading
314 remainingLength = lengthToRead;
315 unsigned int nbFrames = lengthToRead / frameSize;
316 for (i=0;i<nbFrames; i++)
318 Progress = (float)(count+1)/(float)nbFrames;
319 fp->read( raw, frameSize);
321 remainingLength -= frameSize;
324 if (remainingLength !=0 )
325 fp->read( raw, remainingLength);
327 if ( fp->fail() || fp->eof())
329 gdcmWarningMacro( "Reading of Raw pixel data failed." );
333 else if ( IsRLELossless )
335 if ( ! RLEInfo->DecompressRLEFile
336 ( fp, Raw, XSize, YSize, ZSize, TSize, BitsAllocated ) )
338 gdcmWarningMacro( "RLE decompressor failed." );
344 //gdcmWarningMacro( "Sorry, MPEG not yet taken into account" );
346 // fp has already been seek to start of mpeg
347 //ReadMPEGFile(fp, (char*)Raw, PixelDataLength);
352 // Default case concerns JPEG family
353 if ( ! ReadAndDecompressJPEGFile( fp ) )
355 gdcmWarningMacro( "JPEG decompressor ( ReadAndDecompressJPEGFile()"
356 << " method ) failed." );
361 ////////////////////////////////////////////
362 //// Third stage: twigle the bytes and bits.
363 ConvertReorderEndianity();
364 ConvertReArrangeBits();
365 ConvertFixGreyLevels();
366 if (UserFunction) // user is allowed to Mirror, TopDown, Rotate,...the image
367 UserFunction( Raw, FileInternal);
368 ConvertHandleColor();
373 /// Deletes Pixels Area
374 void PixelReadConvert::Squeeze()
390 * \brief Build the RGB image from the Raw image and the LUTs.
392 bool PixelReadConvert::BuildRGBImage()
396 // The job is already done.
402 // The job can't be done
409 // The job can't be done
413 gdcmDebugMacro( "--> BuildRGBImage" );
419 if ( BitsAllocated <= 8 )
421 uint8_t *localRGB = RGB;
422 for (size_t i = 0; i < RawSize; ++i )
425 *localRGB++ = LutRGBA[j];
426 *localRGB++ = LutRGBA[j+1];
427 *localRGB++ = LutRGBA[j+2];
431 else // deal with 16 bits pixels and 16 bits Palette color
433 uint16_t *localRGB = (uint16_t *)RGB;
434 for (size_t i = 0; i < RawSize/2; ++i )
436 j = ((uint16_t *)Raw)[i] * 4;
437 *localRGB++ = ((uint16_t *)LutRGBA)[j];
438 *localRGB++ = ((uint16_t *)LutRGBA)[j+1];
439 *localRGB++ = ((uint16_t *)LutRGBA)[j+2];
446 //-----------------------------------------------------------------------------
449 //-----------------------------------------------------------------------------
452 * \brief Read from file a 12 bits per pixel image and decompress it
453 * into a 16 bits per pixel image.
455 void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp )
456 throw ( FormatError )
458 /// \todo Fix the 3D, 4D pb
459 int nbPixels = XSize * YSize * TSize;
460 uint16_t *localDecompres = (uint16_t*)Raw;
462 for( int p = 0; p < nbPixels; p += 2 )
466 fp->read( (char*)&b0, 1);
467 if ( fp->fail() || fp->eof() )
469 throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
470 "Unfound first block" );
473 fp->read( (char*)&b1, 1 );
474 if ( fp->fail() || fp->eof())
476 throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
477 "Unfound second block" );
480 fp->read( (char*)&b2, 1 );
481 if ( fp->fail() || fp->eof())
483 throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
484 "Unfound second block" );
487 // Two steps are necessary to please VC++
489 // 2 pixels 12bit = [0xABCDEF]
490 // 2 pixels 16bit = [0x0ABD] + [0x0FCE]
492 *localDecompres++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
494 *localDecompres++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
496 /// \todo JPR Troubles expected on Big-Endian processors ?
501 * \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
502 * file and decompress it.
503 * @param fp File Pointer
506 bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp )
510 // make sure this is the right JPEG compression
511 assert( !IsJPEGLossless || !IsJPEGLossy || !IsJPEGLS );
512 // FIXME this is really ugly but it seems I have to load the complete
513 // jpeg2000 stream to use jasper:
514 // I don't think we'll ever be able to deal with multiple fragments properly
516 unsigned long inputlength = 0;
517 JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment();
520 inputlength += jpegfrag->GetLength();
521 jpegfrag = JPEGInfo->GetNextFragment();
523 gdcmAssertMacro( inputlength != 0);
524 uint8_t *inputdata = new uint8_t[inputlength];
525 char *pinputdata = (char*)inputdata;
526 jpegfrag = JPEGInfo->GetFirstFragment();
529 fp->seekg( jpegfrag->GetOffset(), std::ios::beg);
530 fp->read(pinputdata, jpegfrag->GetLength());
531 pinputdata += jpegfrag->GetLength();
532 jpegfrag = JPEGInfo->GetNextFragment();
534 // Warning the inputdata buffer is delete in the function
535 if ( ! gdcm_read_JPEG2000_file( Raw,
536 (char*)inputdata, inputlength ) )
540 // wow what happen, must be an error
541 gdcmWarningMacro( "gdcm_read_JPEG2000_file() failed ");
546 // make sure this is the right JPEG compression
547 assert( !IsJPEGLossless || !IsJPEGLossy || !IsJPEG2000 );
548 // WARNING : JPEG-LS is NOT the 'classical' Jpeg Lossless :
549 // [JPEG-LS is the basis for new lossless/near-lossless compression
550 // standard for continuous-tone images intended for JPEG2000. The standard
551 // is based on the LOCO-I algorithm (LOw COmplexity LOssless COmpression
552 // for Images) developed at Hewlett-Packard Laboratories]
554 // see http://datacompression.info/JPEGLS.shtml
557 std::cerr << "count:" << JPEGInfo->GetFragmentCount() << std::endl;
558 unsigned long inputlength = 0;
559 JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment();
562 inputlength += jpegfrag->GetLength();
563 jpegfrag = JPEGInfo->GetNextFragment();
565 gdcmAssertMacro( inputlength != 0);
566 uint8_t *inputdata = new uint8_t[inputlength];
567 char *pinputdata = (char*)inputdata;
568 jpegfrag = JPEGInfo->GetFirstFragment();
571 fp->seekg( jpegfrag->GetOffset(), std::ios::beg);
572 fp->read(pinputdata, jpegfrag->GetLength());
573 pinputdata += jpegfrag->GetLength();
574 jpegfrag = JPEGInfo->GetNextFragment();
577 //fp->read((char*)Raw, PixelDataLength);
579 std::ofstream out("/tmp/jpegls.jpg");
580 out.write((char*)inputdata, inputlength);
585 gdcmWarningMacro( "Sorry, JPEG-LS not yet taken into account" );
586 fp->seekg( JPEGInfo->GetFirstFragment()->GetOffset(), std::ios::beg);
587 // if ( ! gdcm_read_JPEGLS_file( fp,Raw ) )
592 // make sure this is the right JPEG compression
593 assert( !IsJPEGLS || !IsJPEG2000 );
594 // Precompute the offset localRaw will be shifted with
595 int length = XSize * YSize * ZSize * SamplesPerPixel;
596 int numberBytes = BitsAllocated / 8;
598 // to avoid major troubles when BitsStored == 8 && BitsAllocated==16 !
600 if (BitsStored == 8 && BitsAllocated==16)
605 JPEGInfo->DecompressFromFile(fp, Raw, /*BitsStored*/ dummy , numberBytes, length );
611 * \brief Build Red/Green/Blue/Alpha LUT from File when :
612 * - (0028,0004) : Photometric Interpretation == [PALETTE COLOR ]
614 * - (0028,1101),(0028,1102),(0028,1102)
615 * xxx Palette Color Lookup Table Descriptor are found
617 * - (0028,1201),(0028,1202),(0028,1202)
618 * xxx Palette Color Lookup Table Data - are found
619 * \warning does NOT deal with :
620 * - 0028 1100 Gray Lookup Table Descriptor (Retired)
621 * - 0028 1221 Segmented Red Palette Color Lookup Table Data
622 * - 0028 1222 Segmented Green Palette Color Lookup Table Data
623 * - 0028 1223 Segmented Blue Palette Color Lookup Table Data
624 * no known Dicom reader deals with them :-(
625 * @return a RGBA Lookup Table
627 void PixelReadConvert::BuildLUTRGBA()
630 // Note to code reviewers :
631 // The problem is *much more* complicated, since a lot of manufacturers
632 // Don't follow the norm :
633 // have a look at David Clunie's remark at the end of this .cxx file.
640 // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
642 if ( ! IsPaletteColor )
647 if ( LutRedDescriptor == GDCM_UNFOUND
648 || LutGreenDescriptor == GDCM_UNFOUND
649 || LutBlueDescriptor == GDCM_UNFOUND )
651 gdcmWarningMacro( "(At least) a LUT Descriptor is missing" );
655 ////////////////////////////////////////////
656 // Extract the info from the LUT descriptors
657 int lengthR; // Red LUT length in Bytes
658 int debR; // Subscript of the first Lut Value
659 int nbitsR; // Lut item size (in Bits)
660 int nbRead; // nb of items in LUT descriptor (must be = 3)
662 nbRead = sscanf( LutRedDescriptor.c_str(),
664 &lengthR, &debR, &nbitsR );
667 gdcmWarningMacro( "Wrong Red LUT descriptor" );
669 int lengthG; // Green LUT length in Bytes
670 int debG; // Subscript of the first Lut Value
671 int nbitsG; // Lut item size (in Bits)
673 nbRead = sscanf( LutGreenDescriptor.c_str(),
675 &lengthG, &debG, &nbitsG );
678 gdcmWarningMacro( "Wrong Green LUT descriptor" );
681 int lengthB; // Blue LUT length in Bytes
682 int debB; // Subscript of the first Lut Value
683 int nbitsB; // Lut item size (in Bits)
684 nbRead = sscanf( LutRedDescriptor.c_str(),
686 &lengthB, &debB, &nbitsB );
689 gdcmWarningMacro( "Wrong Blue LUT descriptor" );
692 gdcmDebugMacro(" lengthR " << lengthR << " debR "
693 << debR << " nbitsR " << nbitsR);
694 gdcmDebugMacro(" lengthG " << lengthG << " debG "
695 << debG << " nbitsG " << nbitsG);
696 gdcmDebugMacro(" lengthB " << lengthB << " debB "
697 << debB << " nbitsB " << nbitsB);
699 if ( !lengthR ) // if = 2^16, this shall be 0 see : CP-143
701 if ( !lengthG ) // if = 2^16, this shall be 0
703 if ( !lengthB ) // if = 2^16, this shall be 0
706 ////////////////////////////////////////////////////////
708 if ( ( ! LutRedData ) || ( ! LutGreenData ) || ( ! LutBlueData ) )
710 gdcmWarningMacro( "(At least) a LUT is missing" );
714 // -------------------------------------------------------------
716 if ( BitsAllocated <= 8 )
718 // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
719 LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha)
724 memset( LutRGBA, 0, 1024 );
727 if ( ( nbitsR == 16 ) && ( BitsAllocated == 8 ) )
729 // when LUT item size is different than pixel size
730 mult = 2; // high byte must be = low byte
734 // See PS 3.3-2003 C.11.1.1.2 p 619
738 // if we get a black image, let's just remove the '+1'
739 // from 'i*mult+1' and check again
740 // if it works, we shall have to check the 3 Palettes
741 // to see which byte is ==0 (first one, or second one)
743 // We give up the checking to avoid some (useless ?) overhead
744 // (optimistic asumption)
748 //take "Subscript of the first Lut Value" (debR,debG,debB) into account!
750 //FIXME : +1 : to get 'low value' byte
751 // Trouble expected on Big Endian Processors ?
752 // 16 BIts Per Pixel Palette Color to be swapped?
754 a = LutRGBA + 0 + debR;
755 for( i=0; i < lengthR; ++i )
757 *a = LutRedData[i*mult+1];
761 a = LutRGBA + 1 + debG;
762 for( i=0; i < lengthG; ++i)
764 *a = LutGreenData[i*mult+1];
768 a = LutRGBA + 2 + debB;
769 for(i=0; i < lengthB; ++i)
771 *a = LutBlueData[i*mult+1];
776 for(i=0; i < 256; ++i)
778 *a = 1; // Alpha component
784 // Probabely the same stuff is to be done for 16 Bits Pixels
785 // with 65536 entries LUT ?!?
786 // Still looking for accurate info on the web :-(
788 gdcmWarningMacro( "Sorry Palette Color Lookup Tables not yet dealt with"
789 << " for 16 Bits Per Pixel images" );
791 // forge the 4 * 16 Bits Red/Green/Blue/Alpha LUT
793 LutRGBA = (uint8_t *)new uint16_t[ 65536*4 ]; // 2^16 * 4 (R, G, B, Alpha)
796 memset( LutRGBA, 0, 65536*4*2 ); // 16 bits = 2 bytes ;-)
798 LutItemNumber = 65536;
804 //take "Subscript of the first Lut Value" (debR,debG,debB) into account!
806 a16 = (uint16_t*)LutRGBA + 0 + debR;
807 for( i=0; i < lengthR; ++i )
809 *a16 = ((uint16_t*)LutRedData)[i];
813 a16 = (uint16_t*)LutRGBA + 1 + debG;
814 for( i=0; i < lengthG; ++i)
816 *a16 = ((uint16_t*)LutGreenData)[i];
820 a16 = (uint16_t*)LutRGBA + 2 + debB;
821 for(i=0; i < lengthB; ++i)
823 *a16 = ((uint16_t*)LutBlueData)[i];
827 a16 = (uint16_t*)LutRGBA + 3 ;
828 for(i=0; i < 65536; ++i)
830 *a16 = 1; // Alpha component
833 /* Just to 'see' the LUT, at debug time
834 // Don't remove this commented out code.
836 a16=(uint16_t*)LutRGBA;
837 for (int j=0;j<65536;j++)
839 std::cout << *a16 << " " << *(a16+1) << " "
840 << *(a16+2) << " " << *(a16+3) << std::endl;
848 * \brief Swap the bytes, according to \ref SwapCode.
850 void PixelReadConvert::ConvertSwapZone()
854 // If this file is 'ImplicitVR BigEndian PrivateGE Transfer Syntax',
855 // then the header is in little endian format and the pixel data is in
856 // big endian format. When reading the header, GDCM has already established
857 // a byte swapping code suitable for this machine to read the
858 // header. In TS::ImplicitVRBigEndianPrivateGE, this code will need
859 // to be switched in order to read the pixel data. This must be
860 // done REGARDLESS of the processor endianess!
862 // Example: Assume we are on a little endian machine. When
863 // GDCM reads the header, the header will match the machine
864 // endianess and the swap code will be established as a no-op.
865 // When GDCM reaches the pixel data, it will need to switch the
866 // swap code to do big endian to little endian conversion.
868 // Now, assume we are on a big endian machine. When GDCM reads the
869 // header, the header will be recognized as a different endianess
870 // than the machine endianess, and a swap code will be established
871 // to convert from little endian to big endian. When GDCM readers
872 // the pixel data, the pixel data endianess will now match the
873 // machine endianess. But we currently have a swap code that
874 // converts from little endian to big endian. In this case, we
875 // need to switch the swap code to a no-op.
877 // Therefore, in either case, if the file is in
878 // 'ImplicitVR BigEndian PrivateGE Transfer Syntax', then GDCM needs to switch
879 // the byte swapping code when entering the pixel data.
881 int tempSwapCode = SwapCode;
882 if ( IsPrivateGETransferSyntax )
884 gdcmWarningMacro(" IsPrivateGETransferSyntax found; turn the SwapCode");
885 // PrivateGETransferSyntax only exists for 'true' Dicom images
886 // we assume there is no 'exotic' 32 bits endianess!
887 if (SwapCode == 1234)
891 else if (SwapCode == 4321)
897 if ( BitsAllocated == 16 )
899 uint16_t *im16 = (uint16_t*)Raw;
900 switch( tempSwapCode )
907 for( i = 0; i < RawSize / 2; i++ )
909 im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
913 gdcmWarningMacro("SwapCode value (16 bits) not allowed."
917 else if ( BitsAllocated == 32 )
922 uint32_t *im32 = (uint32_t*)Raw;
923 switch ( tempSwapCode )
928 for( i = 0; i < RawSize / 4; i++ )
930 low = im32[i] & 0x0000ffff; // 4321
931 high = im32[i] >> 16;
932 high = ( high >> 8 ) | ( high << 8 );
933 low = ( low >> 8 ) | ( low << 8 );
935 im32[i] = ( s32 << 16 ) | high;
939 for( i = 0; i < RawSize / 4; i++ )
941 low = im32[i] & 0x0000ffff; // 2143
942 high = im32[i] >> 16;
943 high = ( high >> 8 ) | ( high << 8 );
944 low = ( low >> 8 ) | ( low << 8 );
946 im32[i] = ( s32 << 16 ) | low;
950 for( i = 0; i < RawSize / 4; i++ )
952 low = im32[i] & 0x0000ffff; // 3412
953 high = im32[i] >> 16;
955 im32[i] = ( s32 << 16 ) | high;
959 gdcmWarningMacro("SwapCode value (32 bits) not allowed." << tempSwapCode );
965 * \brief Deal with endianness i.e. re-arange bytes inside the integer
967 void PixelReadConvert::ConvertReorderEndianity()
969 if ( BitsAllocated != 8 )
974 // Special kludge in order to deal with xmedcon broken images:
975 if ( BitsAllocated == 16
976 && BitsStored < BitsAllocated
979 int l = (int)( RawSize / ( BitsAllocated / 8 ) );
980 uint16_t *deb = (uint16_t *)Raw;
981 for(int i = 0; i<l; i++)
983 if ( *deb == 0xffff )
993 * \brief Deal with Grey levels i.e. re-arange them
994 * to have low values = dark, high values = bright
996 void PixelReadConvert::ConvertFixGreyLevels()
1001 uint32_t i; // to please M$VC6
1006 if ( BitsAllocated == 8 )
1008 uint8_t *deb = (uint8_t *)Raw;
1009 for (i=0; i<RawSize; i++)
1017 if ( BitsAllocated == 16 )
1020 for (j=0; j<BitsStored-1; j++)
1022 mask = (mask << 1) +1; // will be fff when BitsStored=12
1025 uint16_t *deb = (uint16_t *)Raw;
1026 for (i=0; i<RawSize/2; i++)
1036 if ( BitsAllocated == 8 )
1038 uint8_t smask8 = 255;
1039 uint8_t *deb = (uint8_t *)Raw;
1040 for (i=0; i<RawSize; i++)
1042 *deb = smask8 - *deb;
1047 if ( BitsAllocated == 16 )
1049 uint16_t smask16 = 65535;
1050 uint16_t *deb = (uint16_t *)Raw;
1051 for (i=0; i<RawSize/2; i++)
1053 *deb = smask16 - *deb;
1062 * \brief Re-arrange the bits within the bytes.
1063 * @return Boolean always true
1065 bool PixelReadConvert::ConvertReArrangeBits() throw ( FormatError )
1068 if ( BitsStored != BitsAllocated )
1070 int l = (int)( RawSize / ( BitsAllocated / 8 ) );
1071 if ( BitsAllocated == 16 )
1073 // pmask : to mask the 'unused bits' (may contain overlays)
1074 uint16_t pmask = 0xffff;
1076 // It's up to the user to remove overlays if any),
1077 // not to gdcm, witout asking !
1078 //pmask = pmask >> ( BitsAllocated - BitsStored );
1080 uint16_t *deb = (uint16_t*)Raw;
1082 if ( !PixelSign ) // Pixels are unsigned
1084 for(int i = 0; i<l; i++)
1087 *deb = (*deb >> (BitsStored - HighBitPosition - 1))/* & pmask */;
1091 else // Pixels are signed
1093 // Hope there is never A
1095 // smask : to check the 'sign' when BitsStored != BitsAllocated
1096 uint16_t smask = 0x0001;
1097 smask = smask << ( 16 - (BitsAllocated - BitsStored + 1) );
1098 // nmask : to propagate sign bit on negative values
1099 int16_t nmask = (int16_t)0x8000;
1100 nmask = nmask >> ( BitsAllocated - BitsStored - 1 );
1102 for(int i = 0; i<l; i++)
1104 *deb = *deb >> (BitsStored - HighBitPosition - 1);
1107 *deb = *deb | nmask;
1111 *deb = *deb & pmask;
1118 else if ( BitsAllocated == 32 )
1126 else if ( BitsAllocated == 32 )
1128 // pmask : to mask the 'unused bits' (may contain overlays)
1129 uint32_t pmask = 0xffffffff;
1130 pmask = pmask >> ( BitsAllocated - BitsStored );
1132 uint32_t *deb = (uint32_t*)Raw;
1136 for(int i = 0; i<l; i++)
1138 *deb = (*deb >> (BitsStored - HighBitPosition - 1)) & pmask;
1144 // smask : to check the 'sign' when BitsStored != BitsAllocated
1145 uint32_t smask = 0x00000001;
1146 smask = smask >> ( 32 - (BitsAllocated - BitsStored +1 ));
1147 // nmask : to propagate sign bit on negative values
1148 int32_t nmask = 0x80000000;
1149 nmask = nmask >> ( BitsAllocated - BitsStored -1 );
1151 for(int i = 0; i<l; i++)
1153 *deb = *deb >> (BitsStored - HighBitPosition - 1);
1155 *deb = *deb | nmask;
1157 *deb = *deb & pmask;
1164 gdcmWarningMacro("Weird image (BitsAllocated !=8, 12, 16, 32)");
1165 throw FormatError( "Weird image !?" );
1172 * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels
1173 * \warning Works on all the frames at a time
1175 void PixelReadConvert::ConvertRGBPlanesToRGBPixels()
1177 gdcmWarningMacro("--> ConvertRGBPlanesToRGBPixels");
1179 uint8_t *localRaw = Raw;
1180 uint8_t *copyRaw = new uint8_t[ RawSize ];
1181 memmove( copyRaw, localRaw, RawSize );
1183 int l = XSize * YSize * ZSize;
1185 uint8_t *a = copyRaw;
1186 uint8_t *b = copyRaw + l;
1187 uint8_t *c = copyRaw + l + l;
1189 for (int j = 0; j < l; j++)
1191 *(localRaw++) = *(a++);
1192 *(localRaw++) = *(b++);
1193 *(localRaw++) = *(c++);
1199 * \brief Convert (cY plane, cB plane, cR plane) to RGB pixels
1200 * \warning Works on all the frames at a time
1202 void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels()
1204 // Remarks for YBR newbees :
1205 // YBR_FULL works very much like RGB, i.e. three samples per pixel,
1206 // just the color space is YCbCr instead of RGB. This is particularly useful
1207 // for doppler ultrasound where most of the image is grayscale
1208 // (i.e. only populates the Y components) and Cb and Cr are mostly zero,
1209 // except for the few patches of color on the image.
1210 // On such images, RLE achieves a compression ratio that is much better
1211 // than the compression ratio on an equivalent RGB image.
1213 gdcmWarningMacro("--> ConvertYcBcRPlanesToRGBPixels");
1215 uint8_t *localRaw = Raw;
1216 uint8_t *copyRaw = new uint8_t[ RawSize ];
1217 memmove( copyRaw, localRaw, RawSize );
1219 // to see the tricks about YBR_FULL, YBR_FULL_422,
1220 // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :
1221 // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
1222 // and be *very* affraid
1225 /// \todo : find an example to see how 3rd dim and 4th dim work together
1226 int l = XSize * YSize * TSize;
1227 int nbFrames = ZSize;
1229 uint8_t *a = copyRaw + 0;
1230 uint8_t *b = copyRaw + l;
1231 uint8_t *c = copyRaw + l+ l;
1234 /// We replaced easy to understand but time consuming floating point
1235 /// computations by the 'well known' integer computation counterpart
1237 /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
1238 /// for code optimisation.
1240 for ( int i = 0; i < nbFrames; i++ )
1242 for ( int j = 0; j < l; j++ )
1244 R = 38142 *(*a-16) + 52298 *(*c -128);
1245 G = 38142 *(*a-16) - 26640 *(*c -128) - 12845 *(*b -128);
1246 B = 38142 *(*a-16) + 66093 *(*b -128);
1255 if (R > 255) R = 255;
1256 if (G > 255) G = 255;
1257 if (B > 255) B = 255;
1259 *(localRaw++) = (uint8_t)R;
1260 *(localRaw++) = (uint8_t)G;
1261 *(localRaw++) = (uint8_t)B;
1270 /// \brief Deals with the color decoding i.e. handle:
1271 /// - R, G, B planes (as opposed to RGB pixels)
1272 /// - YBR (various) encodings.
1273 /// - LUT[s] (or "PALETTE COLOR").
1275 void PixelReadConvert::ConvertHandleColor()
1277 //////////////////////////////////
1278 // Deal with the color decoding i.e. handle:
1279 // - R, G, B planes (as opposed to RGB pixels)
1280 // - YBR (various) encodings.
1281 // - LUT[s] (or "PALETTE COLOR").
1283 // The classification in the color decoding schema is based on the blending
1284 // of two Dicom tags values:
1285 // * "Photometric Interpretation" for which we have the cases:
1286 // - [Photo A] MONOCHROME[1|2] pictures,
1287 // - [Photo B] RGB or YBR_FULL_422 (which acts as RGB),
1288 // - [Photo C] YBR_* (with the above exception of YBR_FULL_422)
1289 // - [Photo D] "PALETTE COLOR" which indicates the presence of LUT[s].
1290 // * "Planar Configuration" for which we have the cases:
1291 // - [Planar 0] 0 then Pixels are already RGB
1292 // - [Planar 1] 1 then we have 3 planes : R, G, B,
1293 // - [Planar 2] 2 then we have 1 gray Plane and 3 LUTs
1295 // Now in theory, one could expect some coherence when blending the above
1296 // cases. For example we should not encounter files belonging at the
1297 // time to case [Planar 0] and case [Photo D].
1298 // Alas, this was only theory ! Because in practice some odd (read ill
1299 // formated Dicom) files (e.g. gdcmData/US-PAL-8-10x-echo.dcm) we encounter:
1300 // - "Planar Configuration" = 0,
1301 // - "Photometric Interpretation" = "PALETTE COLOR".
1302 // Hence gdcm will use the folowing "heuristic" in order to be tolerant
1303 // towards Dicom-non-conformant files:
1304 // << whatever the "Planar Configuration" value might be, a
1305 // "Photometric Interpretation" set to "PALETTE COLOR" forces
1306 // a LUT intervention >>
1308 // Now we are left with the following handling of the cases:
1309 // - [Planar 0] OR [Photo A] no color decoding (since respectively
1310 // Pixels are already RGB and monochrome pictures have no color :),
1311 // - [Planar 1] AND [Photo B] handled with ConvertRGBPlanesToRGBPixels()
1312 // - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels()
1313 // - [Planar 2] OR [Photo D] requires LUT intervention.
1315 gdcmDebugMacro("--> ConvertHandleColor "
1316 << "Planar Configuration " << PlanarConfiguration );
1320 // [Planar 2] OR [Photo D]: LUT intervention done outside
1321 gdcmDebugMacro("--> RawRGB : LUT intervention done outside");
1325 if ( PlanarConfiguration == 1 )
1329 // [Planar 1] AND [Photo C] (remember YBR_FULL_422 acts as RGB)
1330 gdcmDebugMacro("--> YBRFull");
1331 ConvertYcBcRPlanesToRGBPixels();
1335 // [Planar 1] AND [Photo C]
1336 gdcmDebugMacro("--> YBRFull");
1337 ConvertRGBPlanesToRGBPixels();
1342 // When planarConf is 0, and RLELossless (forbidden by Dicom norm)
1343 // pixels need to be RGB-fyied anyway
1347 gdcmDebugMacro("--> RLE Lossless");
1348 ConvertRGBPlanesToRGBPixels();
1351 // In *normal *case, when planarConf is 0, pixels are already in RGB
1354 /// Computes the Pixels Size
1355 void PixelReadConvert::ComputeRawAndRGBSizes()
1357 int bitsAllocated = BitsAllocated;
1358 // Number of "Bits Allocated" is fixed to 16 when it's 12, since
1359 // in this case we will expand the image to 16 bits (see
1360 // \ref ReadAndDecompress12BitsTo16Bits() )
1361 if ( BitsAllocated == 12 )
1366 RawSize = XSize * YSize * ZSize * TSize
1367 * ( bitsAllocated / 8 )
1371 RGBSize = 3 * RawSize; // works for 8 and 16 bits per Pixel
1378 RawSize += RawSize%2;
1379 RGBSize += RGBSize%2;
1382 /// Allocates room for RGB Pixels
1383 void PixelReadConvert::AllocateRGB()
1387 RGB = new uint8_t[RGBSize];
1390 /// Allocates room for RAW Pixels
1391 void PixelReadConvert::AllocateRaw()
1395 Raw = new uint8_t[RawSize];
1398 //-----------------------------------------------------------------------------
1401 * \brief Print self.
1402 * @param indent Indentation string to be prepended during printing.
1403 * @param os Stream to print to.
1405 void PixelReadConvert::Print( std::ostream &os, std::string const &indent )
1408 << "--- Pixel information -------------------------"
1411 << "Pixel Data: offset " << PixelOffset
1412 << " x(" << std::hex << PixelOffset << std::dec
1413 << ") length " << PixelDataLength
1414 << " x(" << std::hex << PixelDataLength << std::dec
1415 << ")" << std::endl;
1417 if ( IsRLELossless )
1421 RLEInfo->Print( os, indent );
1425 gdcmWarningMacro("Set as RLE file but NO RLEinfo present.");
1429 if ( IsJPEG2000 || IsJPEGLossless || IsJPEGLossy || IsJPEGLS )
1433 JPEGInfo->Print( os, indent );
1437 gdcmWarningMacro("Set as JPEG file but NO JPEGinfo present.");
1443 * \brief CallStartMethod
1445 void PixelReadConvert::CallStartMethod()
1449 CommandManager::ExecuteCommand(FH,CMD_STARTPROGRESS);
1453 * \brief CallProgressMethod
1455 void PixelReadConvert::CallProgressMethod()
1457 CommandManager::ExecuteCommand(FH,CMD_PROGRESS);
1461 * \brief CallEndMethod
1463 void PixelReadConvert::CallEndMethod()
1466 CommandManager::ExecuteCommand(FH,CMD_ENDPROGRESS);
1470 //-----------------------------------------------------------------------------
1471 } // end namespace gdcm
1473 // Note to developpers :
1474 // Here is a very detailled post from David Clunie, on the troubles caused
1475 // 'non standard' LUT and LUT description
1476 // We shall have to take it into accound in our code.
1481 Subject: Problem with VOI LUTs in Agfa and Fuji CR and GE DX images, was Re: VOI LUT issues
1482 Date: Sun, 06 Feb 2005 17:13:40 GMT
1483 From: David Clunie <dclunie@dclunie.com>
1484 Reply-To: dclunie@dclunie.com
1485 Newsgroups: comp.protocols.dicom
1486 References: <1107553502.040221.189550@o13g2000cwo.googlegroups.com>
1488 > THE LUT that comes with [my] image claims to be 16-bit, but none of the
1489 > values goes higher than 4095. That being said, though, none of my
1490 > original pixel values goes higher than that, either. I have read
1491 > elsewhere on this group that when that happens you are supposed to
1492 > adjust the LUT. Can someone be more specific? There was a thread from
1493 > 2002 where Marco and David were mentioning doing precisely that.
1500 You have encountered the well known "we know what the standard says but
1501 we are going to ignore it and do what we have been doing for almost
1502 a decade regardless" CR vendor bug. Agfa started this, but they are not
1503 the only vendor doing this now; GE and Fuji may have joined the club.
1505 Sadly, one needs to look at the LUT Data, figure out what the maximum
1506 value actually encoded is, and find the next highest power of 2 (e.g.
1507 212 in this case), to figure out what the range of the data is
1508 supposed to be. I have assumed that if the maximum value in the LUT
1509 data is less than a power of 2 minus 1 (e.g. 0xebc) then the intent
1510 of the vendor was not to use the maximum available grayscale range
1511 of the display (e.g. the maximum is 0xfff in this case). An alternative
1512 would be to scale to the actual maximum rather than a power of two.
1514 Very irritating, and in theory not totally reliable if one really
1515 intended the full 16 bits and only used, say 15, but that is extremely
1516 unlikely since everything would be too dark, and this heuristic
1519 There has never been anything in the standard that describes having
1520 to go through these convolutions. Since the only value in the
1521 standard that describes the bit depth of the LUT values is LUT
1522 Descriptor value 3 and that is (usually) always required to be
1523 either 8 or 16, it mystifies me how the creators' of these images
1524 imagine that the receiver is going to divine the range that is intended. Further, the standard is quite explicit that this 3rd
1525 value defines the range of LUT values, but as far as I am aware, all
1526 the vendors are ignoring the standard and indeed sending a third value
1529 This problem is not confined to CR, and is also seen with DX products.
1531 Typically I have seen:
1533 - Agfa CR, which usually (always ?) sends LUTs, values up to 0x0fff
1534 - Fuji CR, which occasionally send LUTs, values up to 0x03ff
1535 - GE DX, for presentation, which always have LUTs, up to 0x3fff
1537 Swissray, Siemens, Philips, Canon and Kodak never seem to send VOI LUTs
1538 at this point (which is a whole other problem). Note that the presence
1539 or absence of a VOI LUT as opposed to window values may be configurable
1540 on the modality in some cases, and I have just looked at what I happen
1541 to have received from a myriad of sites over whose configuration I have
1542 no control. This may be why the majority of Fuji images have no VOI LUTs,
1543 but a few do (or it may be the Siemens system that these Fuji images went
1544 through that perhaps added it). I do have some test Hologic DX images that
1545 are not from a clinical site that do actually get this right (a value
1546 of 12 for the third value and a max of 0xfff).
1548 Since almost every vendor that I have encountered that encodes LUTs
1549 makes this mistake, perhaps it is time to amend the standard to warn
1550 I did not check presentation states, in which VOI LUTs could also be
1551 encountered, for the prevalence of this mistake, nor did I look at the
1552 encoding of Modality LUT's, which are unusual. Nor did I check digital
1553 mammography images. I would be interested to hear from anyone who has.
1557 PS. The following older thread in this newsgroup discusses this:
1559 "http://groups-beta.google.com/group/comp.protocols.dicom/browse_frm/t hread/6a033444802a35fc/0f0a9a1e35c1468e?q=voi+lut&_done=%2Fgroup%2Fcom p.protocols.dicom%2Fsearch%3Fgroup%3Dcomp.protocols.dicom%26q%3Dvoi+lu t%26qt_g%3D1%26searchnow%3DSearch+this+group%26&_doneTitle=Back+to+Sea rch&&d#0f0a9a1e35c1468e"
1561 PPS. From a historical perspective, the following may be of interest.
1563 In the original standard in 1993, all that was said about this was a
1564 reference to the corresponding such where Modality LUTs are described
1567 "The third value specifies the number of bits for each entry in the
1568 LUT Data. It shall take the value 8 or 16. The LUT Data shall be stored
1569 in a format equivalent to 8 or 16 bits allocated and high bit equal
1572 Since the high bit hint was not apparently explicit enough, a very
1573 early CP, CP 15 (submitted by Agfa as it happens), replaced this with:
1575 "The third value conveys the range of LUT entry values. It shall take
1576 the value 8 or 16, corresponding with the LUT entry value range of
1579 Note: The third value is not required for describing the
1580 LUT data and is only included for informational usage
1581 and for maintaining compatibility with ACRNEMA 2.0.
1583 The LUT Data contains the LUT entry values."
1585 That is how it read in the 1996, 1998 and 1999 editions.
1587 By the 2000 edition, Supplement 33 that introduced presentation states
1588 extensively reworked this entire section and tried to explain this in
1591 "The output range is from 0 to 2^n-1 where n is the third value of LUT
1592 Descriptor. This range is always unsigned."
1594 and also added a note to spell out what the output range meant in the
1597 "9. The output of the Window Center/Width or VOI LUT transformation
1598 is either implicitly scaled to the full range of the display device
1599 if there is no succeeding transformation defined, or implicitly scaled
1600 to the full input range of the succeeding transformation step (such as
1601 the Presentation LUT), if present. See C.11.6.1."
1603 It still reads this way in the 2004 edition.
1605 Note that LUTs in other applications than the general VOI LUT allow for
1606 values other than 8 or 16 in the third value of LUT descriptor to permit
1607 ranges other than 0 to 255 or 65535.
1609 In addition, the DX Image Module specializes the VOI LUT
1610 attributes as follows, in PS 3.3 section C.8.11.3.1.5 (added in Sup 32):
1612 "The third value specifies the number of bits for each entry in the LUT
1613 Data (analogous to ìbits storedî). It shall be between 10-16. The LUT
1614 Data shall be stored in a format equivalent to 16 ìbits allocatedî and
1615 ìhigh bitî equal to ìbits storedî - 1. The third value conveys the range
1616 of LUT entry values. These unsigned LUT entry values shall range between
1617 0 and 2^n-1, where n is the third value of the LUT Descriptor."
1619 So in the case of the GE DX for presentation images, the third value of
1620 LUT descriptor is allowed to be and probably should be 14 rather than 16.