X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=4ccb1e7ae0b52a14856c7b130a601333be791600;hb=ea7eafb27b49a3d467d3d752af40db6e94ebdd13;hp=891a03f862a77fc3b460574652a6912fcbc4f5ff;hpb=c8aac2193a127327cd612e179d1016ad648ef1a2;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 891a03f8..4ccb1e7a 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/11/09 11:21:47 $ - Version: $Revision: 1.304 $ + Date: $Date: 2006/04/11 16:03:26 $ + Version: $Revision: 1.318 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -118,13 +118,14 @@ File::File(): GrPixel = 0x7fe0; // to avoid further troubles NumPixel = 0x0010; BasicOffsetTableItemValue = 0; + FourthDimensionLocation = TagKey(0,0); } /** * \brief Canonical destructor. */ -File::~File () +File::~File() { if ( RLEInfo ) delete RLEInfo; @@ -155,7 +156,6 @@ bool File::Load( ) */ bool File::DoTheLoadingJob( ) { - // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 // We may encounter the 'RETired' (0x0028, 0x0200) tag // (Image Location") . This entry contains the number of @@ -216,6 +216,11 @@ bool File::DoTheLoadingJob( ) // The changed DictEntry will have // - a correct PixelVR OB or OW) // - the name to "Pixel Data" + + //==>Take it easy! + //==> Just change the VR ! + +/* DataEntry *oldEntry = dynamic_cast(entry); if (oldEntry) { @@ -229,24 +234,38 @@ bool File::DoTheLoadingJob( ) // Change only made if usefull if ( PixelVR != oldEntry->GetVR() ) - { - DictEntry* newDict = DictEntry::New(GrPixel,NumPixel, - PixelVR,"1","Pixel Data"); - - DataEntry *newEntry = DataEntry::New(newDict); - newDict->Delete(); - newEntry->Copy(entry); - newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); - oldEntry->SetSelfArea(false); - - RemoveEntry(oldEntry); - AddEntry(newEntry); - newEntry->Delete(); + { + //DictEntry* newDict = DictEntry::New(GrPixel,NumPixel, + // PixelVR,"1","Pixel Data"); + //DataEntry *newEntry = DataEntry::New(newDict); + //newDict->Delete(); + //newEntry->Copy(entry); + //newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); + //oldEntry->SetSelfArea(false); + + //RemoveEntry(oldEntry); + //AddEntry(newEntry); + //newEntry->Delete(); + } } +*/ + VRKey PixelVR; + // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) + // more than 8 (i.e 12, 16) is a 'O Words' + if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) + PixelVR = "OB"; + else + PixelVR = "OW"; + // Change only made if usefull + if ( PixelVR != entry->GetVR() ) + { + entry->SetVR(PixelVR); + } } return true; } + /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current File was properly parsed @@ -451,6 +470,34 @@ int File::GetZSize() return 1; } +/** + * \brief Retrieve the -unnormalized- number of 'times' of '4D image'. + * User has to tell gdcm the location of this '4th Dimension component' + * using SetFourthDimensionLocation() method before. + * \warning The defaulted value is 1. + * @return The encountered size when found, 1 by default + * (The file doesn't contain a '4D image'.). + */ +int File::GetTSize() +{ + if (FourthDimensionLocation == TagKey(0,0) )// 4D location is not set : not a 4D object + return 1; + + DataEntry *entry = GetDataEntry(FourthDimensionLocation.GetGroup(), + FourthDimensionLocation.GetElement() ); + if( !entry ) + { + gdcmWarningMacro( " FourthDimensionLocation not found at : " << + std::hex << FourthDimensionLocation.GetGroup() + << "|" << FourthDimensionLocation.GetElement()); + return 1; + } + else + { + return (int)entry->GetValue(0); + } +} + /** * \brief gets the info from 0018,1164 : ImagerPixelSpacing * then 0028,0030 : Pixel Spacing @@ -512,7 +559,6 @@ float File::GetXSpacing() { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } - return xspacing; } @@ -562,18 +608,17 @@ float File::GetYSpacing() * \brief gets the info from 0018,0088 : Space Between Slices * else from 0018,0050 : Slice Thickness * else 1.0 + * + * When an element is missing, we suppose slices join together + * (no overlapping, no interslice gap) but we have no way to check it ! + * For *Dicom* images, ZSpacing *should be* calculated using + * XOrigin, YOrigin, ZOrigin (of the top left image corner) + * of 2 consecutive images, and the Orientation + * Computing ZSpacing on a single image is not really meaningfull ! * @return Z dimension of a voxel-to be */ float File::GetZSpacing() { - // ---> - // ---> Warning : - // ---> - // For *Dicom* images, ZSpacing should be calculated using - // XOrigin, YOrigin, ZOrigin (of the top left image corner) - // of 2 consecutive images, and the Orientation - // - // Computing ZSpacing on a single image is not really meaningfull ! float zspacing = 1.0f; @@ -601,7 +646,6 @@ float File::GetZSpacing() // if no 'Spacing Between Slices' is found, // we assume slices join together // (no overlapping, no interslice gap) - // if they don't, we're fucked up entry = GetDataEntry(0x0018,0x0050); if( entry ) { @@ -614,6 +658,21 @@ float File::GetZSpacing() else gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); + // if no 'Spacing Between Slices' is found, + // we assume slices join together + // (no overlapping, no interslice gap) + entry = GetDataEntry(0x3004,0x000c); + if( entry ) + { + float z1 = (float)entry->GetValue(0); + float z2 = (float)entry->GetValue(1); + zspacing = z2 - z1; // can be negative... + + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; + } + return zspacing; } @@ -755,16 +814,21 @@ float File::GetZOrigin() /** * \brief gets the info from 0020,0037 : Image Orientation Patient * or from 0020 0035 : Image Orientation (RET) + * * (needed to organize DICOM files based on their x,y,z position) - * @param iop adress of the (6)float array to receive values - * @return true when one of the tag is found - * false when nothing is found + * + * @param iop adress of the (6)float array to receive values. + * (defaulted as 1.,0.,0.,0.,1.,0. if nothing -or inconsistent stuff- + * is found. + * @return true when one of the tag -with consistent values- is found + * false when nothing or inconsistent stuff - is found */ bool File::GetImageOrientationPatient( float iop[6] ) { std::string strImOriPat; //iop is supposed to be float[6] - iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; + iop[0] = iop[4] = 1.; + iop[1] = iop[2] = iop[3] = iop[5] = 0.; // 0020 0037 DS REL Image Orientation (Patient) if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND ) @@ -776,6 +840,7 @@ bool File::GetImageOrientationPatient( float iop[6] ) << " Less than 6 values were found." ); return false; } + return true; } //For ACR-NEMA // 0020 0035 DS REL Image Orientation (RET) @@ -788,8 +853,9 @@ bool File::GetImageOrientationPatient( float iop[6] ) << "Less than 6 values were found." ); return false; } + return true; } - return true; + return false; } /** @@ -1139,7 +1205,7 @@ int File::GetLUTNbits() /** *\brief gets the info from 0028,1052 : Rescale Intercept - * @return Rescale Intercept + * @return Rescale Intercept. defaulted to 0.0 is not found or empty */ float File::GetRescaleIntercept() { @@ -1156,7 +1222,7 @@ float File::GetRescaleIntercept() /** *\brief gets the info from 0028,1053 : Rescale Slope - * @return Rescale Slope + * @return Rescale Slope. defaulted to 1.0 is not found or empty */ float File::GetRescaleSlope() { @@ -1173,7 +1239,7 @@ float File::GetRescaleSlope() /** * \brief This function is intended to user who doesn't want * to have to manage a LUT and expects to get an RBG Pixel image - * (or a monochrome one ...) + * (or a monochrome one, if no LUT found ...) * \warning to be used with GetImagePixels() * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*) */ @@ -1482,7 +1548,7 @@ bool File::Write(std::string fileName, FileType writetype) e0000->SetString(sLen.str()); } - // FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx + /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx if( writetype != JPEG ) { int i_lgPix = GetEntryLength(GrPixel, NumPixel); @@ -1491,7 +1557,7 @@ bool File::Write(std::string fileName, FileType writetype) // no (GrPixel, NumPixel) element std::string s_lgPix = Util::Format("%d", i_lgPix+12); s_lgPix = Util::DicomString( s_lgPix.c_str() ); - InsertEntryString(s_lgPix,GrPixel, 0x0000); + InsertEntryString(s_lgPix,GrPixel, 0x0000, "UL"); } } Document::WriteContent(fp, writetype); @@ -1566,7 +1632,7 @@ void File::ComputeRLEInfo() // Offset Table information on fragments of this current Frame. // Note that the fragment pixels themselves are not loaded // (but just skipped). - long frameOffset = Fp->tellg(); + long frameOffset = Fp->tellg(); // once per fragment uint32_t nbRleSegments = ReadInt32(); if ( nbRleSegments > 16 ) @@ -1613,7 +1679,7 @@ void File::ComputeRLEInfo() // Make sure that we encounter a 'Sequence Delimiter Item' // at the end of the item : - if ( !ReadTag(0xfffe, 0xe0dd) ) + if ( !ReadTag(0xfffe, 0xe0dd) ) // once per RLE File { gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence"); } @@ -1666,7 +1732,7 @@ void File::ComputeJPEGFragmentInfo() i++; } - long fragmentOffset = Fp->tellg(); + long fragmentOffset = Fp->tellg(); // Once per fragment // Store the collected info JPEGFragment *newFragment = new JPEGFragment; newFragment->SetOffset(fragmentOffset); @@ -1699,8 +1765,8 @@ void File::ComputeJPEGFragmentInfo() */ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) { - long positionOnEntry = Fp->tellg(); - long currentPosition = Fp->tellg(); // On debugging purposes + long positionOnEntry = Fp->tellg(); // Only when reading fragments + //long currentPosition = positionOnEntry; // On debugging purposes // Read the Item Tag group and element, and make // sure they are what we expected: @@ -1721,7 +1787,7 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) return false; } if ( itemTagGroup != testGroup || itemTagElem != testElem ) - { + { // in order not to pollute output we don't warn on 'delimitors' if (itemTagGroup != 0xfffe || testGroup != 0xfffe ) gdcmWarningMacro( "Wrong Item Tag found:" @@ -1730,7 +1796,7 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) << " but instead we encountered tag (" << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")" << " at address: " << " 0x(" << std::hex - << (unsigned int)currentPosition << std::dec << ")" + << (unsigned int)positionOnEntry << std::dec << ")" ) ; Fp->seekg(positionOnEntry, std::ios::beg); @@ -1767,10 +1833,12 @@ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) } //// Then read the associated Item Length - long currentPosition = Fp->tellg(); + + // long currentPosition = Fp->tellg(); // save time // JPRx uint32_t itemLength = ReadInt32(); gdcmDebugMacro( "Basic Item Length is: " << itemLength - << " at address: " << std::hex << (unsigned int)currentPosition); +// << " at address: " << std::hex << (unsigned int)currentPosition + ); return itemLength; } @@ -1822,7 +1890,7 @@ void File::ReadEncapsulatedBasicOffsetTable() * @ param fileName file to be open for parsing * @ return false if file cannot be open or no swap info was found, * or no tag was found. - * @ deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead + * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead */ bool File::Load( std::string const &fileName ) {