X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=e108dfdb73add8c7418c99fcd688d8f9d42a7a20;hb=5a7f506da1ee16d6e742c4e95f7f1b09826d8980;hp=09567c0e660712fa93e8a93a08e540106ff1cf6a;hpb=3a0ce54e819134bb3607484194b287df02858775;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 09567c0e..e108dfdb 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2006/08/29 10:21:20 $ - Version: $Revision: 1.325 $ + Date: $Date: 2007/07/03 08:17:24 $ + Version: $Revision: 1.333 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -96,13 +96,13 @@ #include "gdcmRLEFramesInfo.h" #include "gdcmJPEGFragmentsInfo.h" #include "gdcmDataEntry.h" +#include "gdcmSQItem.h" #include #include //sscanf #include // for atoi -namespace gdcm - +namespace GDCM_NAME_SPACE { //----------------------------------------------------------------------------- @@ -473,6 +473,77 @@ int File::GetZSize() return 1; } +// Special case: +// ts["1.2.840.10008.5.1.4.1.1.4.1"] = "Enhanced MR Image Storage"; +bool File::GetSpacing(float &xspacing, float &yspacing, float &zspacing) +{ + xspacing = yspacing = zspacing = 1.0; + TS *ts = Global::GetTS(); + std::string sopclassuid_used; + // D 0002|0002 [UI] [Media Storage SOP Class UID] + + //const std::string &mediastoragesopclassuid_str = GetEntryValue(0x0002,0x0002); + const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002); + const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str); + //D 0008|0016 [UI] [SOP Class UID] + const std::string &sopclassuid_str = GetEntryString(0x0008,0x0016); + const std::string &sopclassuid = ts->GetValue(sopclassuid_str); + if ( mediastoragesopclassuid == GDCM_UNFOUND && sopclassuid == GDCM_UNFOUND ) + { + return false; + } + else + { + if( mediastoragesopclassuid == sopclassuid ) + { + sopclassuid_used = mediastoragesopclassuid; + } + else + { + gdcmWarningMacro( "Inconsistant SOP Class UID: " + << mediastoragesopclassuid << " and " << sopclassuid ); + return false; + } + } + // ok we have now the correc SOP Class UID + if( sopclassuid_used == "Enhanced MR Image Storage" ) + { + SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230); + unsigned int n = PerframeFunctionalGroupsSequence->GetNumberOfSQItems(); + if( !n ) return false; + SQItem *item1 = PerframeFunctionalGroupsSequence->GetFirstSQItem(); + DocEntry *p = item1->GetDocEntry(0x0028,0x9110); + if( !p ) return false; + SeqEntry *seq = dynamic_cast(p); + unsigned int n1 = seq->GetNumberOfSQItems(); + if( !n1 ) return false; + SQItem *item2 = seq->GetFirstSQItem(); + // D 0028|0030 [DS] [Pixel Spacing] [0.83333331346511\0.83333331346511 ] + DocEntry *p2 = item2->GetDocEntry(0x0028,0x0030); + if( !p2 ) return false; + DataEntry *entry = dynamic_cast(p2); + std::string spacing = entry->GetString(); + if ( sscanf( spacing.c_str(), "%f\\%f", &yspacing, &xspacing) != 2 ) + { + xspacing = yspacing = 1.; + return false; + } + // D 0018|0050 [DS] [Slice Thickness] [1 ] + DocEntry *p3 = item2->GetDocEntry(0x0018,0x0050); + if( !p3 ) return false; + DataEntry *entry2 = dynamic_cast(p3); + std::string thickness = entry2->GetString(); + if ( sscanf( thickness.c_str(), "%f", &zspacing) != 1 ) + { + zspacing = 1.; + return false; + } + return true; + } + + return false; + } + /** * \brief Retrieve the -unnormalized- number of 'times' of '4D image'. * User has to tell gdcm the location of this '4th Dimension component' @@ -501,6 +572,8 @@ int File::GetTSize() } } + + /** * \brief gets the info from 0018,1164 : ImagerPixelSpacing * then 0028,0030 : Pixel Spacing @@ -510,9 +583,19 @@ int File::GetTSize() float File::GetXSpacing() { float xspacing = 1.0; + float yspacing = 1.0; + float zspacing = 1.0; + uint32_t nbValue; DataEntry *entry; - bool ok = false; + bool ok = false; + + if ( GetSpacing(xspacing,yspacing,zspacing) ) + { + return xspacing; + } + // else fallback + /* From:David Clunie - view profile Date:Wed, May 24 2006 1:12 pm @@ -658,10 +741,17 @@ and */ float File::GetYSpacing() { - float yspacing; + float xspacing = 1., yspacing = 1.0, zspacing = 1.; uint32_t nbValue; DataEntry *entry; bool ok = false; + + if ( GetSpacing(xspacing,yspacing,zspacing) ) + { + return yspacing; + } + // else fallback + std::string SOPClassUID = GetEntryString(0x0008,0x0016); @@ -762,7 +852,13 @@ float File::GetYSpacing() float File::GetZSpacing() { - float zspacing = 1.0f; + float xspacing = 1.0; + float yspacing = 1.0; + float zspacing = 1.0; + if ( GetSpacing(xspacing,yspacing,zspacing) ) + { + return zspacing; + } // Spacing Between Slices : distance between the middle of 2 slices // Slices may be : @@ -999,6 +1095,122 @@ 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) @@ -1211,6 +1423,9 @@ bool File::IsMonochrome() { gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be " << "mandatory"); + // to deal with old ACR-NEMA images + if (GetNumberOfScalarComponents() == 1) + return true; } return false; } @@ -1352,11 +1567,81 @@ int File::GetLUTNbits() return lutNbits; } +// Special case: +// ts["1.2.840.10008.5.1.4.1.1.4.1"] = "Enhanced MR Image Storage"; + bool File::GetRescaleSlopeIntercept(double &slope, double &intercept) + { + slope = 1.0; + intercept = 0.0; + TS *ts = Global::GetTS(); + std::string sopclassuid_used; + // D 0002|0002 [UI] [Media Storage SOP Class UID] + const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002); + const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str); + //D 0008|0016 [UI] [SOP Class UID] + const std::string &sopclassuid_str = GetEntryString(0x0008,0x0016); + const std::string &sopclassuid = ts->GetValue(sopclassuid_str); + if ( mediastoragesopclassuid == GDCM_UNFOUND && sopclassuid == GDCM_UNFOUND ) + { + return false; + } + else + { + if( mediastoragesopclassuid == sopclassuid ) + { + sopclassuid_used = mediastoragesopclassuid; + } + else + { + gdcmWarningMacro( "Inconsistant SOP Class UID: " + << mediastoragesopclassuid << " and " << sopclassuid ); + return false; + } + } + // ok we have now the correc SOP Class UID + if( sopclassuid_used == "Enhanced MR Image Storage" ) + { + SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230); + unsigned int n = PerframeFunctionalGroupsSequence->GetNumberOfSQItems(); + if( !n ) return false; + SQItem *item1 = PerframeFunctionalGroupsSequence->GetFirstSQItem(); + DocEntry *p = item1->GetDocEntry(0x0028,0x9145); + if( !p ) return false; + SeqEntry *seq = dynamic_cast(p); + unsigned int n1 = seq->GetNumberOfSQItems(); + if( !n1 ) return false; + SQItem *item2 = seq->GetFirstSQItem(); + // D 0028|1052 [DS] [Rescale Intercept] [0 ] + DocEntry *p2 = item2->GetDocEntry(0x0028,0x1052); + if( !p2 ) return false; + DataEntry *entry = dynamic_cast(p2); + std::string intercept_str = entry->GetString(); + if ( sscanf( intercept_str.c_str(), "%lf", &intercept) != 1 ) + { + intercept = 0.; + return false; + } + // D 0028|1053 [DS] [Rescale Slope] [5.65470085470085] + DocEntry *p3 = item2->GetDocEntry(0x0028,0x1053); + if( !p3 ) return false; + DataEntry *entry2 = dynamic_cast(p3); + std::string slope_str = entry2->GetString(); + if ( sscanf( slope_str.c_str(), "%lf", &slope) != 1 ) + { + slope = 1.; + return false; + } + return true; + } + + return false; + } + /** *\brief gets the info from 0028,1052 : Rescale Intercept * @return Rescale Intercept. defaulted to 0.0 is not found or empty */ -float File::GetRescaleIntercept() +double File::GetRescaleIntercept() { // 0028 1052 DS IMG Rescale Intercept DataEntry *entry = GetDataEntry(0x0028, 0x1052); @@ -1373,16 +1658,26 @@ float File::GetRescaleIntercept() *\brief gets the info from 0028,1053 : Rescale Slope * @return Rescale Slope. defaulted to 1.0 is not found or empty */ -float File::GetRescaleSlope() +double File::GetRescaleSlope() { - // 0028 1053 DS IMG Rescale Slope - DataEntry *entry = GetDataEntry(0x0028, 0x1053); - if( !entry ) - { - gdcmDebugMacro( "Missing Rescale Slope (0028,1053)"); - return 1.0f; + double resInter = 0.; + double resSlope = 1.; + if ( GetRescaleSlopeIntercept(resSlope, resInter) ) + { + return resSlope; + } + //0028 1053 DS IMG Rescale Slope + std::string strRescSlope = GetEntryString(0x0028,0x1053); + if ( strRescSlope != GDCM_UNFOUND ) + { + if ( sscanf( strRescSlope.c_str(), "%lf ", &resSlope) != 1 ) + { + // bug in the element 0x0028,0x1053 + gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); + } } - return (float)entry->GetValue(0); + + return resSlope; } /** @@ -1521,7 +1816,7 @@ void File::AnonymizeNoLoad() { std::fstream *fp = new std::fstream(Filename.c_str(), std::ios::in | std::ios::out | std::ios::binary); - gdcm::DocEntry *d; + GDCM_NAME_SPACE::DocEntry *d; uint32_t offset; uint32_t lgth; uint32_t valLgth = 0; @@ -1600,7 +1895,7 @@ bool File::AnonymizeFile() } else { - gdcm::DocEntry *d; + GDCM_NAME_SPACE::DocEntry *d; for (ListElements::iterator it = UserAnonymizeList.begin(); it != UserAnonymizeList.end(); ++it) @@ -1918,7 +2213,7 @@ void File::ComputeJPEGFragmentInfo() * is modified to point after the tag. * On failure (i.e. when the tag wasn't the expected tag * (TestGroup, TestElem) the internal file pointer - * \ref Document::Fp is restored to it's original position. + * \ref Document::Fp is restored to its original position. * @param testGroup The expected group of the tag. * @param testElem The expected Element of the tag. * @return True on success, false otherwise. @@ -1970,10 +2265,10 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) * is placed at the beginning of a tag (TestGroup, TestElement), * read the length associated to the Tag. * \warning On success the internal file pointer \ref Document::Fp - * is modified to point after the tag and it's length. + * is modified to point after the tag and its length. * On failure (i.e. when the tag wasn't the expected tag * (TestGroup, TestElement) the internal file pointer - * \ref Document::Fp is restored to it's original position. + * \ref Document::Fp is restored to its original position. * @param testGroup The expected Group of the tag. * @param testElem The expected Element of the tag. * @return On success returns the length associated to the tag. On failure @@ -2014,7 +2309,7 @@ void File::ReadEncapsulatedBasicOffsetTable() // When present, read the basic offset table itself. // Notes: - since the presence of this basic offset table is optional // we can't rely on it for the implementation, and we will simply - // trash it's content (when present). + // trash its content (when present). // - still, when present, we could add some further checks on the // lengths, but we won't bother with such fuses for the time being. if ( itemLength != 0 )