X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=38282e941cd6878af59f49f9deb65174eb1d6e8a;hb=209f09716365d35c7cdc5b94684d1d1fb00335c7;hp=6d45581b8e9c420d9acb1f1ec63752835e723e80;hpb=195ebc4ca17c18f169cb9ad26162a09b52ab1856;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 6d45581b..38282e94 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2006/03/29 16:13:00 $ - Version: $Revision: 1.317 $ + Date: $Date: 2006/11/15 15:54:15 $ + Version: $Revision: 1.327 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -101,7 +101,8 @@ #include //sscanf #include // for atoi -namespace gdcm +namespace gdcm + { //----------------------------------------------------------------------------- @@ -141,6 +142,7 @@ File::~File() * @return false if file cannot be open or no swap info was found, * or no tag was found. */ + bool File::Load( ) { if ( ! this->Document::Load( ) ) @@ -175,6 +177,7 @@ bool File::DoTheLoadingJob( ) } else { + GrPixel = (uint16_t) atoi( imgLocation.c_str() ); } @@ -216,6 +219,11 @@ 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) { @@ -229,21 +237,34 @@ 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; } @@ -490,10 +511,95 @@ float File::GetXSpacing() { float xspacing = 1.0; uint32_t nbValue; + DataEntry *entry; + bool ok = false; +/* +From:David Clunie - view profile +Date:Wed, May 24 2006 1:12 pm +Email:David Clunie +Groups:comp.protocols.dicom + +The short answer is that: + +- (0018,1164) describes a spacing equivalent to that which + would be measured off a film in projection radiography + +- (0018,7022) does not describe the image pixels themselves, + since detector elements may have been binned to produce + pixels + +- (0018,7020) may be different from (0018,7022) since there + may be non-sensitive material separating individual + detectors (i.e. the size is smaller than the spacing + between centers) + +Only (0018,1164) is relevant when measuring things; the +detector-specific attributes are there to describe the +acquisition. + +David +PS. For ultrasound you need to use Region Calibration. +*/ + +/* +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 Aspect 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 + + ///\todo find images to check if it *actually* works + + if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6") + // Ultrasound Image Storage (Retired) + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1") + // Ultrasound Image Storage + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3") + // Ultrasound Multi-Frame Storage (Retired) + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") ) + // Ultrasound Multi-FrameImage Storage + { + // - check if SOPClassUID contains 2 parts (e.g. "4\3") + // - guess how to deduce the spacing (FOV ?, ??) + + entry = GetDataEntry(0x0028,0x0034); + if ( entry ) + { + nbValue = entry->GetValueCount(); + if( nbValue !=2 ) { + gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) " + << "has a wrong number of values :" << nbValue); + } + xspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ... + ok = true; + } + + if (ok) + return xspacing; + } +/* + if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.1") ) + // Computed Radiography Image Storage + + // CR is in Imager Pixel Spacing (0018,1164)// + +*/ + // go on with old method ... + // --------------------- // To follow David Clunie's advice, we first check ImagerPixelSpacing - DataEntry *entry = GetDataEntry(0x0018,0x1164); + entry = GetDataEntry(0x0018,0x1164); if( entry ) { nbValue = entry->GetValueCount(); @@ -552,10 +658,64 @@ float File::GetXSpacing() */ float File::GetYSpacing() { - float yspacing = 1.0; + float yspacing; + uint32_t nbValue; + DataEntry *entry; + bool ok = false; + + std::string SOPClassUID = GetEntryString(0x0008,0x0016); + + /// \todo check the various SOP Class + /// to get the Pixel Spacing at the proper location + + ///\todo find images to check if it *actually* works + + if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6") + // Ultrasound Image Storage (Retired) + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1") + // Ultrasound Image Storage + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3") + // Ultrasound Multi-Frame Storage (Retired) + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") ) + // Ultrasound Multi-FrameImage Storage + { + // - check if SOPClassUID contains 2 parts (e.g. "4\3") + // - no way to deduce the spacing/ + + entry = GetDataEntry(0x0028,0x0034); + if ( entry ) + { + nbValue = entry->GetValueCount(); + if( nbValue ==2 ) { + yspacing = (float)entry->GetValue(0)/(float)entry->GetValue(1); + //std::cout << "ys " << yspacing << std::endl; + ok = true; + } + else + { + gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) " + << "has a wrong number of values :" << nbValue); + if (nbValue == 0 ) { + ok = false; + } + else if (nbValue == 1 ) { + yspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ... + ok = true; + } + } + } + + if (ok) + return yspacing; + } + + // go on with old method ... + // --------------------- + // To follow David Clunie's advice, we first check ImagerPixelSpacing + yspacing = 1.0; // To follow David Clunie's advice, we first check ImagerPixelSpacing - DataEntry *entry = GetDataEntry(0x0018,0x1164); + entry = GetDataEntry(0x0018,0x1164); if( entry ) { yspacing = (float)entry->GetValue(0); @@ -615,8 +775,7 @@ float File::GetZSpacing() // we suppose slices joint together DataEntry *entry = GetDataEntry(0x0018,0x0088); if( entry ) - { - zspacing = (float)entry->GetValue(0); + { zspacing = (float)entry->GetValue(0); if ( zspacing == 0.0 ) zspacing = 1.0; @@ -840,6 +999,122 @@ bool File::GetImageOrientationPatient( float iop[6] ) return false; } +/** + * \brief gets the cosine of image X axis, against patient X axis + * (Sorry, but Python needs it :-( ) + * @return cosine of image X axis, against patient X axis + */ +float File::GetXCosineOnX() +{ + float iop[6]; + GetImageOrientationPatient( iop ); + return(iop[0]); +} + +/** + * \brief gets the cosine of image X axis, against patient Y axis + * (Sorry, but Python needs it :-( ) + * @return cosine of image X axis, against patient Y axis + */ +float File::GetXCosineOnY() +{ + float iop[6]; + GetImageOrientationPatient( iop ); + return(iop[1]); +} + +/** + * \brief gets the cosine of image X axis, against patient Z axis + * (Sorry, but Python needs it :-( ) + * @return cosine of image X axis, against patient Z axis + */ +float File::GetXCosineOnZ() +{ + float iop[6]; + GetImageOrientationPatient( iop ); + return(iop[2]); +} + +/** + * \brief gets the cosine of image Y axis, against patient X axis + * (Sorry, but Python needs it :-( ) + * @return cosine of image Y axis, against patient X axis + */ +float File::GetYCosineOnX() +{ + float iop[6]; + GetImageOrientationPatient( iop ); + return(iop[3]); +} + +/** + * \brief gets the cosine of image Y axis, against patient Y axis + * (Sorry, but Python needs it :-( ) + * @return cosine of image Y axis, against patient Y axis + */ +float File::GetYCosineOnY() +{ + float iop[6]; + GetImageOrientationPatient( iop ); + return(iop[4]); +} + +/** + * \brief gets the cosine of image Y axis, against patient Z axis + * (Sorry, but Python needs it :-( ) + * @return cosine of image Y axis, against patient Z axis + */ +float File::GetYCosineOnZ() +{ + float iop[6]; + GetImageOrientationPatient( iop ); + return(iop[5]); +} +/** + * \brief gets the info from 0020,0032 : Image Position Patient + * or from 0020 0030 : Image Position (RET) + * + * @param ipp adress of the (3)float array to receive values. + * (defaulted as 0.,0.,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::GetImagePositionPatient( float ipp[3] ) +{ + std::string strImPosiPat; + //ipp is supposed to be float[3] + ipp[0] = ipp[1] = ipp[2] = 0.; + + // 0020 0032 DS REL Image Position (Patient) + strImPosiPat = GetEntryString(0x0020,0x0032); + if ( strImPosiPat != GDCM_UNFOUND ) + { + if ( sscanf( strImPosiPat.c_str(), "%f \\ %f \\%f ", + &ipp[0], &ipp[1], &ipp[2]) != 3 ) + { + gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)." + << " Less than 3 values were found." ); + return false; + } + return true; + } + //For ACR-NEMA + // 0020 0030 DS REL Image Position (RET) + else if ( (strImPosiPat = GetEntryString(0x0020,0x0030)) != GDCM_UNFOUND ) + { + if ( sscanf( strImPosiPat.c_str(), "%f \\ %f \\%f ", + &ipp[0], &ipp[1], &ipp[2]) != 3 ) + { + gdcmWarningMacro( "wrong Image Position Patient (0020,0030). " + << "Less than 3 values were found." ); + return false; + } + return true; + } + return false; +} + /** * \brief Retrieve the number of Bits Stored (actually used) * (as opposed to number of Bits Allocated) @@ -980,21 +1255,29 @@ std::string File::GetPixelType() bitsAlloc = "16"; // default and arbitrary value, not to polute the output } - if ( bitsAlloc == "64" ) + else if ( bitsAlloc == "64" ) { return "FD"; } + // useless since we have to bypass a bug ( >8 && < 16) else if ( bitsAlloc == "12" ) { // It will be unpacked bitsAlloc = "16"; } + else if ( bitsAlloc == "24" ) { // (in order no to be messed up by old RGB images) bitsAlloc = "8"; } - + + int i= atoi(bitsAlloc.c_str()); // fix a bug in some headers + if ( i > 8 && i < 16 ) + { + bitsAlloc = "16"; + } + std::string sign; if( IsSignedPixelData() ) { @@ -1363,6 +1646,10 @@ 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) @@ -1373,13 +1660,20 @@ 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 ); @@ -1539,7 +1833,7 @@ 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); @@ -1866,7 +2160,7 @@ void File::ReadEncapsulatedBasicOffsetTable() // These are the deprecated method that one day should be removed (after the next release) -#ifndef GDCM_LEGACY_REMOVE +//#ifndef GDCM_LEGACY_REMOVE /* * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API) * @ param fileName file to be open for parsing @@ -1874,6 +2168,7 @@ void File::ReadEncapsulatedBasicOffsetTable() * or no tag was found. * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead */ + /* bool File::Load( std::string const &fileName ) { GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2", @@ -1885,7 +2180,7 @@ bool File::Load( std::string const &fileName ) return DoTheLoadingJob( ); } #endif - +*/ //----------------------------------------------------------------------------- // Print