X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=5e83b61d4b9ac97bbe75ffc2490da5c8efddfd5f;hb=0bcc188c6d5185375f809253e8b9b97c856d2eac;hp=2c6928956289de5d23e0a8efa80a097382e54734;hpb=6b4aa7387613d98b62ee41d18aba2dbe0306b4ba;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 2c692895..5e83b61d 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: 2007/09/17 12:16:02 $ + Version: $Revision: 1.337 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -96,12 +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 { //----------------------------------------------------------------------------- @@ -118,13 +119,14 @@ 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 +217,11 @@ 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) { @@ -229,23 +236,36 @@ 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 +470,106 @@ 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' + * 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 @@ -459,11 +579,105 @@ int File::GetZSize() float File::GetXSpacing() { float xspacing = 1.0; + float yspacing = 1.0; + float zspacing = 1.0; + uint32_t nbValue; + DataEntry *entry; + 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 +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(); @@ -471,7 +685,7 @@ float File::GetXSpacing() if( nbValue !=2 ) gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) " << "has a wrong number of values :" << nbValue); - + if( nbValue >= 3 ) xspacing = (float)entry->GetValue(2); else if( nbValue >= 2 ) @@ -495,7 +709,7 @@ float File::GetXSpacing() if( nbValue !=2 ) gdcmWarningMacro("PixelSpacing (0x0018,0x0030) " << "has a wrong number of values :" << nbValue); - + if( nbValue >= 3 ) xspacing = (float)entry->GetValue(2); else if( nbValue >= 2 ) @@ -511,7 +725,6 @@ float File::GetXSpacing() { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } - return xspacing; } @@ -523,10 +736,69 @@ float File::GetXSpacing() */ float File::GetYSpacing() { - float yspacing = 1.0; + 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); + + /// \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); @@ -568,13 +840,18 @@ 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() { - 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 : @@ -587,8 +864,7 @@ 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; @@ -768,15 +1044,19 @@ 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 +1070,7 @@ 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 +1083,125 @@ bool File::GetImageOrientationPatient( double iop[6] ) << "Less than 6 values were found." ); return false; } + return true; } - return true; + 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; } /** @@ -946,21 +1344,29 @@ 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() ) { @@ -1010,6 +1416,9 @@ 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; } @@ -1151,11 +1560,80 @@ 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 + * @return Rescale Intercept. defaulted to 0.0 if not found or empty */ -float File::GetRescaleIntercept() +double File::GetRescaleIntercept() { // 0028 1052 DS IMG Rescale Intercept DataEntry *entry = GetDataEntry(0x0028, 0x1052); @@ -1170,24 +1648,34 @@ float File::GetRescaleIntercept() /** *\brief gets the info from 0028,1053 : Rescale Slope - * @return Rescale Slope + * @return Rescale Slope. defaulted to 1.0 if 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; } /** * \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*) */ @@ -1320,7 +1808,7 @@ 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; @@ -1329,6 +1817,10 @@ 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) @@ -1340,12 +1832,19 @@ void File::AnonymizeNoLoad() 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 ); @@ -1388,7 +1887,7 @@ bool File::AnonymizeFile() } else { - gdcm::DocEntry *d; + GDCM_NAME_SPACE::DocEntry *d; for (ListElements::iterator it = UserAnonymizeList.begin(); it != UserAnonymizeList.end(); ++it) @@ -1479,6 +1978,7 @@ bool File::AnonymizeFile() */ bool File::Write(std::string fileName, FileType writetype) { + gdcmDebugMacro(" File::Write "); std::ofstream *fp = new std::ofstream(fileName.c_str(), std::ios::out | std::ios::binary); if (*fp == NULL) @@ -1496,16 +1996,16 @@ bool File::Write(std::string fileName, FileType writetype) e0000->SetString(sLen.str()); } - // FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx - if( writetype != JPEG ) + /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx + if( writetype != JPEG && writetype != JPEG2000) { int i_lgPix = GetEntryLength(GrPixel, NumPixel); - if (i_lgPix != -2) + if (i_lgPix != -2) /// \todo wtf "-2" ?!? { // 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); @@ -1524,7 +2024,7 @@ bool File::Write(std::string fileName, FileType writetype) // Private /** * \brief Parse pixel data from disk of [multi-]fragment RLE encoding. - * Compute the RLE extra information and store it in \ref RLEInfo + * Compute the RLE extra information and store it in RLEInfo * for later pixel retrieval usage. */ void File::ComputeRLEInfo() @@ -1580,7 +2080,7 @@ 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 +2127,7 @@ 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"); } @@ -1636,7 +2136,7 @@ void File::ComputeRLEInfo() /** * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding. * Compute the jpeg extra information (fragment[s] offset[s] and - * length) and store it[them] in \ref JPEGInfo for later pixel + * length) and store it[them] in JPEGInfo for later pixel * retrieval usage. */ void File::ComputeJPEGFragmentInfo() @@ -1680,7 +2180,7 @@ 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); @@ -1699,22 +2199,22 @@ void File::ComputeJPEGFragmentInfo() } /** - * \brief Assuming the internal file pointer \ref Document::Fp + * \brief Assuming the internal file pointer Document::Fp * is placed at the beginning of a tag, check whether this * tag is (TestGroup, TestElem). - * \warning On success the internal file pointer \ref Document::Fp + * \warning On success the internal file pointer Document::Fp * 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. + * 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. */ 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 +2235,7 @@ 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 +2244,7 @@ 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); @@ -1754,14 +2254,14 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) } /** - * \brief Assuming the internal file pointer \ref Document::Fp + * \brief Assuming the internal file pointer Document::Fp * 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. + * \warning On success the internal file pointer Document::Fp + * 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. + * 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 @@ -1781,10 +2281,12 @@ 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; } @@ -1800,7 +2302,7 @@ 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 ) @@ -1836,7 +2338,7 @@ 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 +2351,8 @@ bool File::Load( std::string const &fileName ) return DoTheLoadingJob( ); } +#endif */ -//#endif - //----------------------------------------------------------------------------- // Print