X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=acc5acfae523a4f2e110f0972f1f657e1b244aeb;hb=e7768bbebdc9a5972e396d71a3e848f5674ee378;hp=fe54402e1fddbfd7358d8603e2c873d0032decce;hpb=1d9ac5cec02b9daa18b16835882b531731b125ad;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index fe54402e..acc5acfa 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/10/18 12:58:28 $ - Version: $Revision: 1.277 $ + Date: $Date: 2007/10/23 15:52:33 $ + Version: $Revision: 1.341 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -19,21 +19,21 @@ // // -------------- Remember ! ---------------------------------- // -// Image Position Patient (0020,0032): +// Image Position (Patient) (0020,0032): // If not found (ACR_NEMA) we try Image Position (0020,0030) // If not found (ACR-NEMA), we consider Slice Location (0020,1041) // or Location (0020,0050) // as the Z coordinate, // 0. for all the coordinates if nothing is found // -// Image Position (Patient) (0020,0032) VM=3 What is it used for? +// Image Position (Patient) (0020,0032) VM=3 // --> // The attribute Patient Orientation (0020,0020) from the General Image Module // is of type 2C and has the condition Required if image does not require // Image Orientation (0020,0037) and Image Position (0020,0032). // However, if the image does require the attributes // - Image Orientation (Patient) (0020,0037), VM=6 -// - Image Position Patient (0020,0032), VM=3 +// - Image Position (Patient) (0020,0032), VM=3 // then attribute Patient Orientation (0020,0020) should not be present // in the images. // @@ -65,7 +65,7 @@ // FFDR = Feet First-Decubitus Right // FFDL = Feet First-Decubitus Left -// we can also find +// we can also find (non standard!) // SEMIERECT // SUPINE @@ -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; @@ -155,7 +157,6 @@ 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 +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) { @@ -230,21 +236,36 @@ bool File::DoTheLoadingJob( ) // Change only made if usefull if ( PixelVR != oldEntry->GetVR() ) { - DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel, - PixelVR,"1","Pixel Data"); - - DataEntry *newEntry = new DataEntry(newDict); - newEntry->Copy(entry); - newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); - oldEntry->SetSelfArea(false); - - RemoveEntry(oldEntry); - AddEntry(newEntry); + //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 @@ -449,6 +470,104 @@ 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 @@ -458,17 +577,116 @@ 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(); + // Can't use IsValueCountValid because of the complex heuristic. + if( nbValue !=2 ) + gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) " + << "has a wrong number of values :" << nbValue); + if( nbValue >= 3 ) xspacing = (float)entry->GetValue(2); - if( nbValue >= 2 ) + else if( nbValue >= 2 ) xspacing = (float)entry->GetValue(1); else xspacing = (float)entry->GetValue(0); @@ -479,35 +697,20 @@ float File::GetXSpacing() } else { - gdcmWarningMacro( "Unfound Pixel Spacing (0018,1164)" ); + gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); } -/* const std::string &strImagerPixelSpacing = GetEntryString(0x0018,0x1164); - if ( strImagerPixelSpacing != GDCM_UNFOUND ) - { - if ( ( nbValues = sscanf( strImagerPixelSpacing.c_str(), - "%f\\%f", &yspacing, &xspacing)) != 2 ) - { - // if no values, xspacing is set to 1.0 - if ( nbValues == 0 ) - xspacing = 1.0; - // if single value is found, xspacing is defaulted to yspacing - if ( nbValues == 1 ) - xspacing = yspacing; - - if ( xspacing == 0.0 ) - xspacing = 1.0; - } - return xspacing; - }*/ - entry = GetDataEntry(0x0028,0x0030); if( entry ) { nbValue = entry->GetValueCount(); + if( nbValue !=2 ) + gdcmWarningMacro("PixelSpacing (0x0018,0x0030) " + << "has a wrong number of values :" << nbValue); + if( nbValue >= 3 ) xspacing = (float)entry->GetValue(2); - if( nbValue >= 2 ) + else if( nbValue >= 2 ) xspacing = (float)entry->GetValue(1); else xspacing = (float)entry->GetValue(0); @@ -520,42 +723,6 @@ float File::GetXSpacing() { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } - -/* const std::string &strSpacing = GetEntryString(0x0028,0x0030); - if ( strSpacing == GDCM_UNFOUND ) - { - gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); - return 1.; - } - - if ( ( nbValues = sscanf( strSpacing.c_str(), - "%f \\%f ", &yspacing, &xspacing)) != 2 ) - { - // if no values, xspacing is set to 1.0 - if ( nbValues == 0 ) - xspacing = 1.0; - // if single value is found, xspacing is defaulted to yspacing - if ( nbValues == 1 ) - xspacing = yspacing; - - if ( xspacing == 0.0 ) - xspacing = 1.0; - return xspacing; - - }*/ - - // to avoid troubles with David Clunie's-like images (at least one) -/* if ( xspacing == 0.0 && yspacing == 0.0) - return 1.0; - - if ( xspacing == 0.0) - { - gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm-like problem"); - // seems to be a bug in the header ... - nbValues = sscanf( strSpacing.c_str(), "%f \\0\\%f ", &yspacing, &xspacing); - gdcmAssertMacro( nbValues == 2 ); - } -*/ return xspacing; } @@ -567,10 +734,69 @@ 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); @@ -581,22 +807,8 @@ float File::GetYSpacing() } else { - gdcmWarningMacro( "Unfound Pixel Spacing (0018,1164)" ); + gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); } -/* const std::string &strImagerPixelSpacing = GetEntryString(0x0018,0x1164); - if ( strImagerPixelSpacing != GDCM_UNFOUND ) - { - nbValues = sscanf( strImagerPixelSpacing.c_str(), "%f", &yspacing); - - // if sscanf cannot read any float value, it won't affect yspacing - if ( nbValues == 0 ) - yspacing = 1.0; - - if ( yspacing == 0.0 ) - yspacing = 1.0; - - return yspacing; - }*/ entry = GetDataEntry(0x0028,0x0030); if( entry ) @@ -611,22 +823,6 @@ float File::GetYSpacing() { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } -/* std::string strSpacing = GetEntryString(0x0028,0x0030); - if ( strSpacing == GDCM_UNFOUND ) - { - gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)"); - return 1.; - } - - // if sscanf cannot read any float value, it won't affect yspacing - nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing); - - // if no values, yspacing is set to 1.0 - if ( nbValues == 0 ) - yspacing = 1.0; - - if ( yspacing == 0.0 ) - yspacing = 1.0;*/ return yspacing; } @@ -635,20 +831,25 @@ 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; + 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 : @@ -661,8 +862,7 @@ 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; @@ -674,7 +874,6 @@ 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 ) { @@ -687,32 +886,22 @@ float File::GetZSpacing() else gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); - return zspacing; - -/* const std::string &strSpacingBSlices = GetEntryString(0x0018,0x0088); - if ( strSpacingBSlices == GDCM_UNFOUND ) + // if no 'Spacing Between Slices' is found, + // we assume slices join together + // (no overlapping, no interslice gap) + entry = GetDataEntry(0x3004,0x000c); + if( entry ) { - gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); - const std::string &strSliceThickness = GetEntryString(0x0018,0x0050); - if ( strSliceThickness == GDCM_UNFOUND ) - { - gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); - return 1.0; - } - else - { - // 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 - return (float)atof( strSliceThickness.c_str() ); - } + 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; } - - float zsp = (float)atof( strSpacingBSlices.c_str()); - if (zsp == 0.0) // last change not to break further computations ... - zsp = 1.0; - return zsp;*/ + + return zspacing; } /** @@ -736,27 +925,14 @@ float File::GetXOrigin() } if( entry->GetValueCount() == 3 ) - return (float)entry->GetValue(0); - return 0.0f; - -/* std::string strImPos = GetEntryString(0x0020,0x0032); - if ( strImPos == GDCM_UNFOUND ) { - gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); - strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos == GDCM_UNFOUND ) + if (!entry->IsValueCountValid() ) { - gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); - return 0.0; + gdcmErrorMacro( "Invalid Value Count" ); } + return (float)entry->GetValue(0); } - - if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 ) - { - return 0.0; - } - - return xImPos;*/ + return 0.0f; } /** @@ -780,28 +956,14 @@ float File::GetYOrigin() } if( entry->GetValueCount() == 3 ) - return (float)entry->GetValue(1); - return 0.0f; -/* float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryString(0x0020,0x0032); - - if ( strImPos == GDCM_UNFOUND) { - gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); - strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos == GDCM_UNFOUND ) + if (!entry->IsValueCountValid() ) { - gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); - return 0.; - } - } - - if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 ) - { - return 0.; + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(1); } - - return yImPos;*/ + return 0.0f; } /** @@ -818,113 +980,83 @@ float File::GetZOrigin() if( entry ) { if( entry->GetValueCount() == 3 ) - return (float)entry->GetValue(0); + { + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(2); + } gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); return 0.0f; } -/* float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryString(0x0020,0x0032); - - if ( strImPos != GDCM_UNFOUND ) - { - if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3) - { - gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); - return 0.; // bug in the element 0x0020,0x0032 - } - else - { - return zImPos; - } - }*/ entry = GetDataEntry(0x0020,0x0030); if( entry ) { if( entry->GetValueCount() == 3 ) - return (float)entry->GetValue(0); + { + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(2); + } gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); return 0.0f; } -/* strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos != GDCM_UNFOUND ) - { - if ( sscanf( strImPos.c_str(), - "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos ) != 3 ) - { - gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); - return 0.; // bug in the element 0x0020,0x0032 - } - else - { - return zImPos; - } - }*/ // for *very* old ACR-NEMA images entry = GetDataEntry(0x0020,0x1041); if( entry ) { if( entry->GetValueCount() == 1 ) - return (float)entry->GetValue(0); - gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); - return 0.0f; - } -/* std::string strSliceLocation = GetEntryString(0x0020,0x1041); - if ( strSliceLocation != GDCM_UNFOUND ) - { - if ( sscanf( strSliceLocation.c_str(), "%f ", &zImPos) != 1) { - gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); - return 0.; // bug in the element 0x0020,0x1041 - } - else - { - return zImPos; + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(0); // VM=1 ! } + gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); + return 0.0f; } - gdcmWarningMacro( "Unfound Slice Location (0020,1041)");*/ entry = GetDataEntry(0x0020,0x0050); if( entry ) { - gdcmWarningMacro( "Unfound Location (0020,0050)"); if( entry->GetValueCount() == 1 ) + { + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(0); + } gdcmWarningMacro( "Wrong Location (0020,0050)"); return 0.0f; } -/* std::string strLocation = GetEntryString(0x0020,0x0050); - if ( strLocation != GDCM_UNFOUND ) - { - if ( sscanf( strLocation.c_str(), "%f ", &zImPos) != 1 ) - { - gdcmWarningMacro( "Wrong Location (0020,0050)"); - return 0.; // bug in the element 0x0020,0x0050 - } - else - { - return zImPos; - } - } - gdcmWarningMacro( "Unfound Location (0020,0050)");*/ - return 0.; // Hopeless } /** * \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 ) @@ -936,6 +1068,7 @@ 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) @@ -948,11 +1081,126 @@ bool File::GetImageOrientationPatient( float 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; +} /** * \brief Retrieve the number of Bits Stored (actually used) @@ -965,19 +1213,10 @@ int File::GetBitsStored() DataEntry *entry = GetDataEntry(0x0028,0x0101); if( !entry ) { - gdcmWarningMacro("(0028,0101) is supposed to be mandatory"); + gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory"); return 0; } return (int)entry->GetValue(0); - -/* std::string strSize = GetEntryString( 0x0028, 0x0101 ); - if ( strSize == GDCM_UNFOUND ) - { - gdcmWarningMacro("(0028,0101) is supposed to be mandatory"); - return 0; // It's supposed to be mandatory - // the caller will have to check - } - return atoi( strSize.c_str() );*/ } /** @@ -991,19 +1230,10 @@ int File::GetBitsAllocated() DataEntry *entry = GetDataEntry(0x0028,0x0100); if( !entry ) { - gdcmWarningMacro("(0028,0100) is supposed to be mandatory"); + gdcmWarningMacro("BitsAllocated (0028,0100) is supposed to be mandatory"); return 0; } return (int)entry->GetValue(0); - -/* std::string strSize = GetEntryString(0x0028,0x0100); - if ( strSize == GDCM_UNFOUND ) - { - gdcmWarningMacro( "(0028,0100) is supposed to be mandatory"); - return 0; // It's supposed to be mandatory - // the caller will have to check - } - return atoi( strSize.c_str() );*/ } /** @@ -1017,18 +1247,10 @@ int File::GetHighBitPosition() DataEntry *entry = GetDataEntry(0x0028,0x0102); if( !entry ) { - gdcmWarningMacro("(0028,0102) is supposed to be mandatory"); + gdcmWarningMacro("HighBitPosition (0028,0102) is supposed to be mandatory"); return 0; } return (int)entry->GetValue(0); - -/* std::string strSize = GetEntryString( 0x0028, 0x0102 ); - if ( strSize == GDCM_UNFOUND ) - { - gdcmWarningMacro( "(0028,0102) is supposed to be mandatory"); - return 0; - } - return atoi( strSize.c_str() );*/ } /** @@ -1042,20 +1264,11 @@ int File::GetSamplesPerPixel() DataEntry *entry = GetDataEntry(0x0028,0x0002); if( !entry ) { - gdcmWarningMacro("(0028,0002) is supposed to be mandatory"); + gdcmWarningMacro("SamplesPerPixel (0028,0002) is supposed to be mandatory"); return 1; // Well, it's supposed to be mandatory ... // but sometimes it's missing : *we* assume Gray pixels } return (int)entry->GetValue(0); - -/* const std::string &strSize = GetEntryString(0x0028,0x0002); - if ( strSize == GDCM_UNFOUND ) - { - gdcmWarningMacro( "(0028,0002) is supposed to be mandatory"); - return 1; // Well, it's supposed to be mandatory ... - // but sometimes it's missing : *we* assume Gray pixels - } - return atoi( strSize.c_str() );*/ } /** @@ -1068,18 +1281,9 @@ int File::GetPlanarConfiguration() DataEntry *entry = GetDataEntry(0x0028,0x0006); if( !entry ) { - gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); return 0; } return (int)entry->GetValue(0); - -/* std::string strSize = GetEntryString(0x0028,0x0006); - if ( strSize == GDCM_UNFOUND ) - { - gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); - return 0; - } - return atoi( strSize.c_str() );*/ } /** @@ -1134,72 +1338,42 @@ std::string File::GetPixelType() std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { - gdcmWarningMacro( "Missing Bits Allocated (0028,0100)"); + gdcmWarningMacro( "Bits Allocated (0028,0100) supposed to be mandatory"); 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"; } - std::string sign; - if( IsSignedPixelData() ) - { - sign = "S"; - } - else + int i= atoi(bitsAlloc.c_str()); // fix a bug in some headers + if ( i > 8 && i < 16 ) { - sign = "U"; - } - -/* std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated - if ( bitsAlloc == GDCM_UNFOUND ) - { - gdcmWarningMacro( "Missing Bits Allocated (0028,0100)"); - bitsAlloc = "16"; // default and arbitrary value, not to polute the output - } - - if ( bitsAlloc == "64" ) - { - return "FD"; - } - 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"; - } - - std::string sign = GetEntryString(0x0028, 0x0103);//"Pixel Representation" - if (sign == GDCM_UNFOUND ) + std::string sign; + if( IsSignedPixelData() ) { - gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); - sign = "U"; // default and arbitrary value, not to polute the output + sign = "S"; } - else if ( sign == "0" ) + else { sign = "U"; } - else - { - sign = "S"; - }*/ return bitsAlloc + sign; } @@ -1216,22 +1390,11 @@ bool File::IsSignedPixelData() DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation" if( !entry ) { - gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); + gdcmWarningMacro( "Pixel Representation (0028,0103) supposed to be " + << "mandatory"); return false; } return entry->GetValue(0) != 0; -/* std::string strSign = GetEntryString( 0x0028, 0x0103 ); - if ( strSign == GDCM_UNFOUND ) - { - gdcmWarningMacro( "(0028,0103) is supposed to be mandatory"); - return false; - } - int sign = atoi( strSign.c_str() ); - if ( sign == 0 ) - { - return false; - } - return true;*/ } /** @@ -1249,7 +1412,11 @@ bool File::IsMonochrome() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); + gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be " + << "mandatory"); + // to deal with old ACR-NEMA images + if (GetNumberOfScalarComponents() == 1) + return true; } return false; } @@ -1268,7 +1435,8 @@ bool File::IsMonochrome1() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); + gdcmWarningMacro( "Photometric Interpretation (0028,0004) : supposed to" + << " be mandatory! "); } return false; } @@ -1285,9 +1453,16 @@ bool File::IsPaletteColor() { return true; } + + // MONOCHROME + [Enhanced CT Image Storage] actually have Palettes + std::string sopClassUid = GetEntryString( 0x0008, 0x0016 ); + if (Util::DicomStringEqual( sopClassUid, "1.2.840.10008.5.1.4.1.1.2.1")) + { + return true; + } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : Palette color (0028,0004)"); + gdcmDebugMacro( "Not found : Palette color (0028,0004)"); } return false; } @@ -1299,14 +1474,14 @@ bool File::IsPaletteColor() */ bool File::IsYBRFull() { - std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); + std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "YBR_FULL" ) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : YBR Full (0028,0004)"); + gdcmDebugMacro( "Not found : YBR Full (0028,0004)"); } return false; } @@ -1338,7 +1513,13 @@ bool File::HasLUT() return false; } // Red Palette Color Lookup Table Data - if ( !GetDocEntry(0x0028,0x1201) ) + bool segmented; + segmented = GetDocEntry(0x0028,0x1221) && + GetDocEntry(0x0028,0x1222) && + GetDocEntry(0x0028,0x1223); + if( segmented ) return true; + + if( !GetDocEntry(0x0028,0x1201) ) { return false; } @@ -1390,11 +1571,80 @@ 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); @@ -1405,54 +1655,38 @@ float File::GetRescaleIntercept() } return (float)entry->GetValue(0); -/* float resInter = 0.; - /// 0028 1052 DS IMG Rescale Intercept - const std::string &strRescInter = GetEntryString(0x0028,0x1052); - if ( strRescInter != GDCM_UNFOUND ) - { - if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 ) - { - // bug in the element 0x0028,0x1052 - gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." ); - } - } - - return resInter;*/ } /** *\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 ) - { - gdcmWarningMacro( "Missing Rescale Slope (0028,1053)"); - return 1.0f; - } - return (float)entry->GetValue(0); -/* float resSlope = 1.; + 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(), "%f ", &resSlope) != 1 ) + if ( sscanf( strRescSlope.c_str(), "%lf ", &resSlope) != 1 ) { // bug in the element 0x0028,0x1053 gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); } } - return resSlope;*/ + 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*) */ @@ -1533,7 +1767,7 @@ size_t File::GetPixelOffset() } else { - gdcmDebugMacro( "Big trouble : Pixel Element (" + gdcmWarningMacro( "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); return 0; } @@ -1555,7 +1789,7 @@ size_t File::GetPixelAreaLength() } else { - gdcmDebugMacro( "Big trouble : Pixel Element (" + gdcmWarningMacro( "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); return 0; } @@ -1570,7 +1804,7 @@ size_t File::GetPixelAreaLength() void File::AddAnonymizeElement (uint16_t group, uint16_t elem, std::string const &value) { - Element el; + DicomElement el; el.Group = group; el.Elem = elem; el.Value = value; @@ -1585,7 +1819,7 @@ 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; @@ -1594,6 +1828,10 @@ 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) @@ -1605,12 +1843,19 @@ 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 ); @@ -1653,7 +1898,7 @@ bool File::AnonymizeFile() } else { - gdcm::DocEntry *d; + GDCM_NAME_SPACE::DocEntry *d; for (ListElements::iterator it = UserAnonymizeList.begin(); it != UserAnonymizeList.end(); ++it) @@ -1744,6 +1989,7 @@ 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) @@ -1761,16 +2007,19 @@ bool File::Write(std::string fileName, FileType writetype) e0000->SetString(sLen.str()); } - int i_lgPix = GetEntryLength(GrPixel, NumPixel); - if (i_lgPix != -2) + /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx + if( writetype != JPEG && writetype != JPEG2000) { - // 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); + int i_lgPix = GetEntryLength(GrPixel, NumPixel); + 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, "UL"); + } } - - Document::WriteContent(fp, writetype); + Document::WriteContent(fp, writetype,false,false); fp->close(); delete fp; @@ -1786,7 +2035,7 @@ 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() @@ -1842,7 +2091,7 @@ 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 ) @@ -1889,7 +2138,7 @@ 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"); } @@ -1898,7 +2147,7 @@ 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() @@ -1942,7 +2191,7 @@ 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); @@ -1961,22 +2210,22 @@ void File::ComputeJPEGFragmentInfo() } /** - * \brief Assuming the internal file pointer \ref Document::Fp - * is placed at the beginning of a tag check whether this + * \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: @@ -1987,20 +2236,27 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) itemTagGroup = ReadInt16(); itemTagElem = ReadInt16(); } - catch ( FormatError /*e*/ ) + catch ( FormatError ) { - //std::cerr << e << std::endl; + gdcmErrorMacro( "Can not read tag for " + << " We should have found tag (" + << DictEntry::TranslateToKey(testGroup,testElem) << ")" + ) ; + return false; } if ( itemTagGroup != testGroup || itemTagElem != testElem ) { - gdcmWarningMacro( "Wrong Item Tag found:" - << " We should have found tag (" - << std::hex << testGroup << "," << testElem << ")" << std::endl - << " but instead we encountered tag (" - << std::hex << itemTagGroup << "," << itemTagElem << ")" - << " at address: " << " 0x(" << (unsigned int)currentPosition << ")" - ) ; + // in order not to pollute output we don't warn on 'delimitors' + if (itemTagGroup != 0xfffe || testGroup != 0xfffe ) + gdcmWarningMacro( "Wrong Item Tag found:" + << " We should have found tag (" + << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl + << " but instead we encountered tag (" + << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")" + << " at address: " << " 0x(" << std::hex + << (unsigned int)positionOnEntry << std::dec << ")" + ) ; Fp->seekg(positionOnEntry, std::ios::beg); return false; @@ -2009,14 +2265,14 @@ 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 @@ -2027,17 +2283,21 @@ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) if ( !ReadTag(testGroup, testElem) ) { + // Avoid polutting output + if ( testGroup != 0xfffe ) + gdcmErrorMacro( "ReadTag did not succeed for (" + << DictEntry::TranslateToKey(testGroup,testElem) + << ")..." ); return 0; } //// Then read the associated Item Length - long currentPosition = Fp->tellg(); + + // long currentPosition = Fp->tellg(); // save time // JPRx uint32_t itemLength = ReadInt32(); - { - gdcmWarningMacro( "Basic Item Length is: " - << itemLength << std::endl - << " at address: " << std::hex << (unsigned int)currentPosition); - } + gdcmDebugMacro( "Basic Item Length is: " << itemLength +// << " at address: " << std::hex << (unsigned int)currentPosition + ); return itemLength; } @@ -2053,7 +2313,7 @@ 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 ) @@ -2071,9 +2331,9 @@ void File::ReadEncapsulatedBasicOffsetTable() uint32_t val = BasicOffsetTableItemValue[i]; BasicOffsetTableItemValue[i] = ( (val<<24) | ((val<<8) & 0x00ff0000) | - ((val>>8) & 0x0000ff00) | (val>>24) ); + ( (val>>8) & 0x0000ff00) | (val>>24) ); #endif - gdcmWarningMacro( "Read one length for: " << + gdcmDebugMacro( "Read one length for: " << std::hex << BasicOffsetTableItemValue[i] ); } @@ -2083,29 +2343,15 @@ void File::ReadEncapsulatedBasicOffsetTable() // These are the deprecated method that one day should be removed (after the next release) -#ifndef GDCM_LEGACY_REMOVE -/** - * \brief Constructor (DEPRECATED : temporaryly kept not to break the API) - * @param filename name of the file whose header we want to analyze - * @deprecated do not use any longer - */ -File::File( std::string const &filename ) - :Document( ) -{ - RLEInfo = new RLEFramesInfo; - JPEGInfo = new JPEGFragmentsInfo; - - SetFileName( filename ); - Load( ); // gdcm::Document is first Loaded, then the 'File part' -} - -/** - * \brief Loader. (DEPRECATED : temporaryly kept not to break the API) - * @param fileName file to be open for parsing - * @return false if file cannot be open or no swap info was found, +//#ifndef GDCM_LEGACY_REMOVE +/* + * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API) + * @ 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 */ + /* bool File::Load( std::string const &fileName ) { GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2", @@ -2117,7 +2363,7 @@ bool File::Load( std::string const &fileName ) return DoTheLoadingJob( ); } #endif - +*/ //----------------------------------------------------------------------------- // Print