X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=38282e941cd6878af59f49f9deb65174eb1d6e8a;hb=209f09716365d35c7cdc5b94684d1d1fb00335c7;hp=2d76f3f0a5e4a38d9ad4734b02a6bd4192e8ff32;hpb=8e5be16bcfd2ba5a93e2692d39add1bc7bfedaf8;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 2d76f3f0..38282e94 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/10/25 14:36:30 $ - Version: $Revision: 1.294 $ + Date: $Date: 2006/11/15 15:54:15 $ + Version: $Revision: 1.327 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -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 @@ -101,7 +101,8 @@ #include //sscanf #include // for atoi -namespace gdcm +namespace gdcm + { //----------------------------------------------------------------------------- @@ -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; @@ -140,6 +142,7 @@ File::~File () * @return false if file cannot be open or no swap info was found, * or no tag was found. */ + bool File::Load( ) { if ( ! this->Document::Load( ) ) @@ -155,7 +158,6 @@ 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 @@ -175,6 +177,7 @@ bool File::DoTheLoadingJob( ) } else { + GrPixel = (uint16_t) atoi( imgLocation.c_str() ); } @@ -216,6 +219,11 @@ bool File::DoTheLoadingJob( ) // The changed DictEntry will have // - a correct PixelVR OB or OW) // - the name to "Pixel Data" + + //==>Take it easy! + //==> Just change the VR ! + +/* DataEntry *oldEntry = dynamic_cast(entry); if (oldEntry) { @@ -229,24 +237,38 @@ bool File::DoTheLoadingJob( ) // Change only made if usefull if ( PixelVR != oldEntry->GetVR() ) - { - DictEntry* newDict = DictEntry::New(GrPixel,NumPixel, - PixelVR,"1","Pixel Data"); - - DataEntry *newEntry = DataEntry::New(newDict); - newDict->Delete(); - newEntry->Copy(entry); - newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); - oldEntry->SetSelfArea(false); - - RemoveEntry(oldEntry); - AddEntry(newEntry); - newEntry->Delete(); + { + //DictEntry* newDict = DictEntry::New(GrPixel,NumPixel, + // PixelVR,"1","Pixel Data"); + //DataEntry *newEntry = DataEntry::New(newDict); + //newDict->Delete(); + //newEntry->Copy(entry); + //newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); + //oldEntry->SetSelfArea(false); + + //RemoveEntry(oldEntry); + //AddEntry(newEntry); + //newEntry->Delete(); + } } +*/ + VRKey PixelVR; + // 8 bits allocated is a 'OB(ytes)' , as well as 24 (old ACR-NEMA RGB) + // more than 8 (i.e 12, 16) is a 'OW(ords)' + if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) + PixelVR = "OB"; + else + PixelVR = "OW"; + // Change only made if usefull + if ( PixelVR != entry->GetVR() ) + { + entry->SetVR(PixelVR); + } } return true; } + /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current File was properly parsed @@ -451,6 +473,34 @@ int File::GetZSize() return 1; } +/** + * \brief Retrieve the -unnormalized- number of 'times' of '4D image'. + * User has to tell gdcm the location of this '4th Dimension component' + * using SetFourthDimensionLocation() method before. + * \warning The defaulted value is 1. + * @return The encountered size when found, 1 by default + * (The file doesn't contain a '4D image'.). + */ +int File::GetTSize() +{ + if (FourthDimensionLocation == TagKey(0,0) )// 4D location is not set : not a 4D object + return 1; + + DataEntry *entry = GetDataEntry(FourthDimensionLocation.GetGroup(), + FourthDimensionLocation.GetElement() ); + if( !entry ) + { + gdcmWarningMacro( " FourthDimensionLocation not found at : " << + std::hex << FourthDimensionLocation.GetGroup() + << "|" << FourthDimensionLocation.GetElement()); + return 1; + } + else + { + return (int)entry->GetValue(0); + } +} + /** * \brief gets the info from 0018,1164 : ImagerPixelSpacing * then 0028,0030 : Pixel Spacing @@ -461,17 +511,106 @@ float File::GetXSpacing() { float xspacing = 1.0; uint32_t nbValue; + DataEntry *entry; + bool ok = false; +/* +From:David Clunie - view profile +Date:Wed, May 24 2006 1:12 pm +Email:David Clunie +Groups:comp.protocols.dicom + +The short answer is that: + +- (0018,1164) describes a spacing equivalent to that which + would be measured off a film in projection radiography + +- (0018,7022) does not describe the image pixels themselves, + since detector elements may have been binned to produce + pixels + +- (0018,7020) may be different from (0018,7022) since there + may be non-sensitive material separating individual + detectors (i.e. the size is smaller than the spacing + between centers) + +Only (0018,1164) is relevant when measuring things; the +detector-specific attributes are there to describe the +acquisition. + +David + +PS. For ultrasound you need to use Region Calibration. +*/ + +/* +It *SHOULD* first find the IOD and then deduce which tags to read +Eg: Cross section this is in Pixel Spacing (0028,0030) +CR is in Imager Pixel Spacing (0018,1164) +US is in Pixel Aspect Ratio (0028,0034) +RT is in : +(3002,0011) Image Plane Pixel Spacing +(3002,0012) RT Image Position +and +(3004,000c) for deducing Z spacing +*/ + + std::string SOPClassUID = GetEntryString(0x0008,0x0016); + + /// \todo check the various SOP Class + /// to get the Pixel Spacing at the proper location + + ///\todo find images to check if it *actually* works + + if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6") + // Ultrasound Image Storage (Retired) + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1") + // Ultrasound Image Storage + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3") + // Ultrasound Multi-Frame Storage (Retired) + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") ) + // Ultrasound Multi-FrameImage Storage + { + // - check if SOPClassUID contains 2 parts (e.g. "4\3") + // - guess how to deduce the spacing (FOV ?, ??) + + entry = GetDataEntry(0x0028,0x0034); + if ( entry ) + { + nbValue = entry->GetValueCount(); + if( nbValue !=2 ) { + gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) " + << "has a wrong number of values :" << nbValue); + } + xspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ... + ok = true; + } + + if (ok) + return xspacing; + } +/* + if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.1") ) + // Computed Radiography Image Storage + // CR is in Imager Pixel Spacing (0018,1164)// + +*/ + // go on with old method ... + // --------------------- // To follow David Clunie's advice, we first check ImagerPixelSpacing - DataEntry *entry = GetDataEntry(0x0018,0x1164); + entry = GetDataEntry(0x0018,0x1164); if( entry ) { nbValue = entry->GetValueCount(); // 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); @@ -489,6 +628,10 @@ float File::GetXSpacing() 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); else if( nbValue >= 2 ) @@ -504,7 +647,6 @@ float File::GetXSpacing() { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } - return xspacing; } @@ -516,10 +658,64 @@ float File::GetXSpacing() */ float File::GetYSpacing() { - float yspacing = 1.0; + float yspacing; + uint32_t nbValue; + DataEntry *entry; + bool ok = false; + + std::string SOPClassUID = GetEntryString(0x0008,0x0016); + + /// \todo check the various SOP Class + /// to get the Pixel Spacing at the proper location + + ///\todo find images to check if it *actually* works + + if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6") + // Ultrasound Image Storage (Retired) + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1") + // Ultrasound Image Storage + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3") + // Ultrasound Multi-Frame Storage (Retired) + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") ) + // Ultrasound Multi-FrameImage Storage + { + // - check if SOPClassUID contains 2 parts (e.g. "4\3") + // - no way to deduce the spacing/ + + entry = GetDataEntry(0x0028,0x0034); + if ( entry ) + { + nbValue = entry->GetValueCount(); + if( nbValue ==2 ) { + yspacing = (float)entry->GetValue(0)/(float)entry->GetValue(1); + //std::cout << "ys " << yspacing << std::endl; + ok = true; + } + else + { + gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) " + << "has a wrong number of values :" << nbValue); + if (nbValue == 0 ) { + ok = false; + } + else if (nbValue == 1 ) { + yspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ... + ok = true; + } + } + } + + if (ok) + return yspacing; + } + + // go on with old method ... + // --------------------- + // To follow David Clunie's advice, we first check ImagerPixelSpacing + yspacing = 1.0; // To follow David Clunie's advice, we first check ImagerPixelSpacing - DataEntry *entry = GetDataEntry(0x0018,0x1164); + entry = GetDataEntry(0x0018,0x1164); if( entry ) { yspacing = (float)entry->GetValue(0); @@ -554,18 +750,17 @@ 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; @@ -580,8 +775,7 @@ float File::GetZSpacing() // we suppose slices joint together DataEntry *entry = GetDataEntry(0x0018,0x0088); if( entry ) - { - zspacing = (float)entry->GetValue(0); + { zspacing = (float)entry->GetValue(0); if ( zspacing == 0.0 ) zspacing = 1.0; @@ -593,7 +787,6 @@ 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 ) { @@ -606,6 +799,21 @@ float File::GetZSpacing() else gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); + // if no 'Spacing Between Slices' is found, + // we assume slices join together + // (no overlapping, no interslice gap) + entry = GetDataEntry(0x3004,0x000c); + if( entry ) + { + 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; + } + return zspacing; } @@ -631,7 +839,10 @@ float File::GetXOrigin() if( entry->GetValueCount() == 3 ) { - gdcmErrorMacro( entry->IsValueCountValid() ); + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(0); } return 0.0f; @@ -659,7 +870,10 @@ float File::GetYOrigin() if( entry->GetValueCount() == 3 ) { - gdcmErrorMacro( entry->IsValueCountValid() ); + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(1); } return 0.0f; @@ -680,7 +894,10 @@ float File::GetZOrigin() { if( entry->GetValueCount() == 3 ) { - gdcmErrorMacro( entry->IsValueCountValid() ); + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(2); } gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); @@ -692,7 +909,10 @@ float File::GetZOrigin() { if( entry->GetValueCount() == 3 ) { - gdcmErrorMacro( entry->IsValueCountValid() ); + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(2); } gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); @@ -705,7 +925,10 @@ float File::GetZOrigin() { if( entry->GetValueCount() == 1 ) { - gdcmErrorMacro( entry->IsValueCountValid() ); + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(0); // VM=1 ! } gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); @@ -717,7 +940,10 @@ float File::GetZOrigin() { if( entry->GetValueCount() == 1 ) { - gdcmErrorMacro( entry->IsValueCountValid() ); + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(0); } gdcmWarningMacro( "Wrong Location (0020,0050)"); @@ -729,16 +955,21 @@ 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( 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 ) @@ -750,6 +981,7 @@ 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) @@ -762,8 +994,125 @@ 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; } /** @@ -777,7 +1126,7 @@ 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); @@ -794,7 +1143,7 @@ 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); @@ -811,7 +1160,7 @@ 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); @@ -828,7 +1177,7 @@ 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 } @@ -845,7 +1194,6 @@ int File::GetPlanarConfiguration() DataEntry *entry = GetDataEntry(0x0028,0x0006); if( !entry ) { - gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); return 0; } return (int)entry->GetValue(0); @@ -903,25 +1251,33 @@ 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"; } - + + int i= atoi(bitsAlloc.c_str()); // fix a bug in some headers + if ( i > 8 && i < 16 ) + { + bitsAlloc = "16"; + } + std::string sign; if( IsSignedPixelData() ) { @@ -947,7 +1303,8 @@ 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; @@ -968,7 +1325,8 @@ bool File::IsMonochrome() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); + gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be " + << "mandatory"); } return false; } @@ -987,7 +1345,8 @@ 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; } @@ -1006,7 +1365,7 @@ bool File::IsPaletteColor() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : Palette color (0028,0004)"); + gdcmDebugMacro( "Not found : Palette color (0028,0004)"); } return false; } @@ -1025,7 +1384,7 @@ bool File::IsYBRFull() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : YBR Full (0028,0004)"); + gdcmDebugMacro( "Not found : YBR Full (0028,0004)"); } return false; } @@ -1111,7 +1470,7 @@ int File::GetLUTNbits() /** *\brief gets the info from 0028,1052 : Rescale Intercept - * @return Rescale Intercept + * @return Rescale Intercept. defaulted to 0.0 is not found or empty */ float File::GetRescaleIntercept() { @@ -1128,7 +1487,7 @@ float File::GetRescaleIntercept() /** *\brief gets the info from 0028,1053 : Rescale Slope - * @return Rescale Slope + * @return Rescale Slope. defaulted to 1.0 is not found or empty */ float File::GetRescaleSlope() { @@ -1136,7 +1495,7 @@ float File::GetRescaleSlope() DataEntry *entry = GetDataEntry(0x0028, 0x1053); if( !entry ) { - gdcmWarningMacro( "Missing Rescale Slope (0028,1053)"); + gdcmDebugMacro( "Missing Rescale Slope (0028,1053)"); return 1.0f; } return (float)entry->GetValue(0); @@ -1145,7 +1504,7 @@ float File::GetRescaleSlope() /** * \brief This function is intended to user who doesn't want * to have to manage a LUT and expects to get an RBG Pixel image - * (or a monochrome one ...) + * (or a monochrome one, if no LUT found ...) * \warning to be used with GetImagePixels() * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*) */ @@ -1226,7 +1585,7 @@ size_t File::GetPixelOffset() } else { - gdcmDebugMacro( "Big trouble : Pixel Element (" + gdcmWarningMacro( "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); return 0; } @@ -1248,7 +1607,7 @@ size_t File::GetPixelAreaLength() } else { - gdcmDebugMacro( "Big trouble : Pixel Element (" + gdcmWarningMacro( "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); return 0; } @@ -1287,6 +1646,10 @@ void File::AnonymizeNoLoad() it != UserAnonymizeList.end(); ++it) { + + //std::cout << "File::AnonymizeNoLoad -------" << std::hex <<(*it).Group <<"|"<< + // (*it).Elem + // << "[" << (*it).Value << "] "<< std::dec << std::endl; d = GetDocEntry( (*it).Group, (*it).Elem); if ( d == NULL) @@ -1297,13 +1660,20 @@ void File::AnonymizeNoLoad() gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); continue; } + + valLgth = (*it).Value.size(); + if (valLgth == 0) + continue; offset = d->GetOffset(); lgth = d->GetLength(); + + //std::cout << "lgth " << lgth << " valLgth " << valLgth << std::endl; if (valLgth < lgth) { spaces = new std::string( lgth-valLgth, ' '); (*it).Value = (*it).Value + *spaces; + //std::cout << "[" << (*it).Value << "] " << lgth << std::endl; delete spaces; } fp->seekp( offset, std::ios::beg ); @@ -1454,19 +1824,18 @@ bool File::Write(std::string fileName, FileType writetype) e0000->SetString(sLen.str()); } - // Derma?.dcm does not have it...let's remove it FIXME FIXME + /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx if( writetype != JPEG ) - { - int i_lgPix = GetEntryLength(GrPixel, NumPixel); - if (i_lgPix != -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); - } - } - + { + int i_lgPix = GetEntryLength(GrPixel, NumPixel); + if (i_lgPix != -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); fp->close(); @@ -1539,7 +1908,7 @@ 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 ) @@ -1586,7 +1955,7 @@ 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"); } @@ -1639,7 +2008,7 @@ 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); @@ -1672,8 +2041,8 @@ void File::ComputeJPEGFragmentInfo() */ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) { - long positionOnEntry = Fp->tellg(); - long currentPosition = Fp->tellg(); // On debugging purposes + long positionOnEntry = Fp->tellg(); // Only when reading fragments + //long currentPosition = positionOnEntry; // On debugging purposes // Read the Item Tag group and element, and make // sure they are what we expected: @@ -1694,16 +2063,16 @@ 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 ) - gdcmErrorMacro( "Wrong Item Tag found:" + 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)currentPosition << std::dec << ")" + << (unsigned int)positionOnEntry << std::dec << ")" ) ; Fp->seekg(positionOnEntry, std::ios::beg); @@ -1740,10 +2109,12 @@ 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; } @@ -1777,9 +2148,9 @@ 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] ); } @@ -1789,29 +2160,15 @@ 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' -} - +//#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 + * @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", @@ -1823,7 +2180,7 @@ bool File::Load( std::string const &fileName ) return DoTheLoadingJob( ); } #endif - +*/ //----------------------------------------------------------------------------- // Print