X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=9c55ec89dbe7b06e16f140041949b297a6d1e656;hb=3f244b54d3cff8a8ccbb2f8586ba992618075b41;hp=2c6928956289de5d23e0a8efa80a097382e54734;hpb=6b4aa7387613d98b62ee41d18aba2dbe0306b4ba;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 2c692895..9c55ec89 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/11/25 13:56:31 $ - Version: $Revision: 1.309 $ + Date: $Date: 2006/06/08 13:37:33 $ + Version: $Revision: 1.321 $ 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; @@ -215,6 +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) { @@ -228,24 +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 'OB(ytes)' , as well as 24 (old ACR-NEMA RGB) + // more than 8 (i.e 12, 16) is a 'OW(ords)' + 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 @@ -450,6 +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 @@ -460,6 +508,36 @@ float File::GetXSpacing() { float xspacing = 1.0; uint32_t nbValue; + +/* +It *SHOULD* first find the IOD and then deduce which tags to read +Eg: Cross section this is in Pixel Spacing (0028,0030) +CR is in Imager Pixel Spacing (0018,1164) +US is in Pixel Ratio (0028,0034) +RT is in : +(3002,0011) Image Plane Pixel Spacing +(3002,0012) RT Image Position +and +(3004,000c) for deducing Z spacing +*/ + + +// std::string SOPClassUID = GetEntryString(0x0008,0x0016); + + /// \todo check the various SOP Class + /// to get the Pixel Spacing at the proper location + + + // Ultrasound Image Storage (Retired) +/* + if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6") + { + - check if SOPClassUID contains 2 parts (e.g. "4\3") + - guess how to deduce the spacing (FOV ?, ??) + } + else + // go on with old method ... +*/ // To follow David Clunie's advice, we first check ImagerPixelSpacing @@ -511,7 +589,6 @@ float File::GetXSpacing() { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } - return xspacing; } @@ -568,7 +645,6 @@ float File::GetYSpacing() * 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() @@ -768,15 +844,19 @@ 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( double iop[6] ) +bool File::GetImageOrientationPatient( float iop[6] ) { std::string strImOriPat; - //iop is supposed to be double[6] + //iop is supposed to be float[6] iop[0] = iop[4] = 1.; iop[1] = iop[2] = iop[3] = iop[5] = 0.; @@ -790,6 +870,7 @@ bool File::GetImageOrientationPatient( double iop[6] ) << " Less than 6 values were found." ); return false; } + return true; } //For ACR-NEMA // 0020 0035 DS REL Image Orientation (RET) @@ -802,8 +883,9 @@ bool File::GetImageOrientationPatient( double iop[6] ) << "Less than 6 values were found." ); return false; } + return true; } - return true; + return false; } /** @@ -1153,7 +1235,7 @@ 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() { @@ -1170,7 +1252,7 @@ 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() { @@ -1187,7 +1269,7 @@ 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*) */ @@ -1329,6 +1411,10 @@ void File::AnonymizeNoLoad() it != UserAnonymizeList.end(); ++it) { + + //std::cout << "File::AnonymizeNoLoad -------" << std::hex <<(*it).Group <<"|"<< + // (*it).Elem + // << "[" << (*it).Value << "] "<< std::dec << std::endl; d = GetDocEntry( (*it).Group, (*it).Elem); if ( d == NULL) @@ -1339,13 +1425,20 @@ void File::AnonymizeNoLoad() gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); continue; } + + valLgth = (*it).Value.size(); + if (valLgth == 0) + continue; offset = d->GetOffset(); lgth = d->GetLength(); + + //std::cout << "lgth " << lgth << " valLgth " << valLgth << std::endl; if (valLgth < lgth) { spaces = new std::string( lgth-valLgth, ' '); (*it).Value = (*it).Value + *spaces; + //std::cout << "[" << (*it).Value << "] " << lgth << std::endl; delete spaces; } fp->seekp( offset, std::ios::beg ); @@ -1496,7 +1589,7 @@ 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); @@ -1505,7 +1598,7 @@ 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); @@ -1580,7 +1673,7 @@ 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 ) @@ -1627,7 +1720,7 @@ 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"); } @@ -1680,7 +1773,7 @@ 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); @@ -1713,8 +1806,8 @@ 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: @@ -1735,7 +1828,7 @@ 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:" @@ -1744,7 +1837,7 @@ 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); @@ -1781,10 +1874,12 @@ 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; } @@ -1836,7 +1931,7 @@ 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 ) @@ -1849,9 +1944,8 @@ bool File::Load( std::string const &fileName ) return DoTheLoadingJob( ); } +#endif */ -//#endif - //----------------------------------------------------------------------------- // Print