X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=b26c57d831b59495ceb2d1c672dbccbe757b29c4;hb=2bfcd91b06ec416462da3f080917576cc8793c18;hp=fda7c94f9011bc1967a208a8373d0c9372823b9e;hpb=e022eedb7541761440c9f21343db626d918d4980;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index fda7c94f..b26c57d8 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/02/10 10:12:16 $ - Version: $Revision: 1.220 $ + Date: $Date: 2005/10/23 15:26:43 $ + Version: $Revision: 1.289 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -26,6 +26,65 @@ // 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? +// --> +// 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 +// then attribute Patient Orientation (0020,0020) should not be present +// in the images. +// +// Remember also : +// Patient Position (0018,5100) values : + +// HFS = Head First-Supine, where increasing (positive axis direction) : +// X -> to the direction pointed to by the patient's oustretched left arm +// Y -> to the anterior-to-posterior direction in the patient's body +// Z -> to the feet-to-head direction in the patient's body + +// HFP = Head First-Prone, where increasing (positive axis direction) : +// X -> to the direction pointed to by the patient's oustretched left arm +// Y -> to the anterior-to-posterior direction in the patient's body +// Z -> to the feet-to-head direction in the patient's body + +// FFS = Feet First-Supine, where increasing (positive axis direction) : +// X -> to the direction pointed to by the patient's oustretched left arm +// Y -> to the anterior-to-posterion direction in the patient's body +// Z -> to the feet-to-head direction in the patient's body + +// FFP = Feet First-Prone, where increasing (positive axis direction) : +// X -> to the direction pointed to by the patient's oustretched left arm +// Y -> to the posterior-to-anterior direction in the patient's body +// Z -> to the feet-to-head direction in the patient's body + +// HFDR = Head First-Decubitus Right +// HFDL = Head First-Decubitus Left +// FFDR = Feet First-Decubitus Right +// FFDL = Feet First-Decubitus Left + +// we can also find + +// SEMIERECT +// SUPINE + +// CS 2 Patient Orientation (0020 0020) +// When the coordinates of the image +// are always present, this field is almost never used. +// Better we don't trust it too much ... +// Found Values are : +// L\P +// L\FP +// P\F +// L\F +// P\FR +// R\F +// +// (0020|0037) [Image Orientation (Patient)] [1\0\0\0\1\0 ] + + // --------------------------------------------------------------- // #include "gdcmFile.h" @@ -33,28 +92,69 @@ #include "gdcmUtil.h" #include "gdcmDebug.h" #include "gdcmTS.h" -#include "gdcmValEntry.h" -#include "gdcmBinEntry.h" #include "gdcmSeqEntry.h" #include "gdcmRLEFramesInfo.h" #include "gdcmJPEGFragmentsInfo.h" +#include "gdcmDataEntry.h" -#include //sscanf #include +#include //sscanf +#include // for atoi namespace gdcm { + //----------------------------------------------------------------------------- // Constructor / Destructor + /** - * \brief Constructor - * @param filename name of the file whose header we want to analyze + * \brief Constructor used when we want to generate dicom files from scratch */ -File::File( std::string const &filename ) - :Document( filename ) -{ +File::File(): + Document() +{ RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; + GrPixel = 0x7fe0; // to avoid further troubles + NumPixel = 0x0010; + BasicOffsetTableItemValue = 0; +} + + +/** + * \brief Canonical destructor. + */ +File::~File () +{ + if ( RLEInfo ) + delete RLEInfo; + if ( JPEGInfo ) + delete JPEGInfo; + delete[] BasicOffsetTableItemValue; +} + +//----------------------------------------------------------------------------- +// Public +/** + * \brief Loader + * @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( ) ) + return false; + + return DoTheLoadingJob( ); +} + +/** + * \brief Does the Loading Job (internal use only) + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool File::DoTheLoadingJob( ) +{ // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 // We may encounter the 'RETired' (0x0028, 0x0200) tag @@ -67,7 +167,7 @@ File::File( std::string const &filename ) // Note: this IS the right place for the code // Image Location - const std::string &imgLocation = GetEntryValue(0x0028, 0x0200); + const std::string &imgLocation = GetEntryString(0x0028, 0x0200); if ( imgLocation == GDCM_UNFOUND ) { // default value @@ -104,7 +204,7 @@ File::File( std::string const &filename ) { // Compute the RLE or JPEG info OpenFile(); - std::string ts = GetTransferSyntax(); + const std::string &ts = GetTransferSyntax(); Fp->seekg( entry->GetOffset(), std::ios::beg ); if ( Global::GetTS()->IsRLELossless(ts) ) ComputeRLEInfo(); @@ -112,15 +212,14 @@ File::File( std::string const &filename ) ComputeJPEGFragmentInfo(); CloseFile(); - // Create a new BinEntry to change the the DictEntry + // Create a new DataEntry to change the DictEntry // The changed DictEntry will have // - a correct PixelVR OB or OW) - // - a VM to "PXL" // - the name to "Pixel Data" - BinEntry *oldEntry = dynamic_cast(entry); - if(oldEntry) + DataEntry *oldEntry = dynamic_cast(entry); + if (oldEntry) { - std::string PixelVR; + VRKey PixelVR; // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) // more than 8 (i.e 12, 16) is a 'O Words' if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) @@ -129,12 +228,13 @@ File::File( std::string const &filename ) PixelVR = "OW"; // Change only made if usefull - if( PixelVR != oldEntry->GetVR() ) + if ( PixelVR != oldEntry->GetVR() ) { - DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel, - PixelVR,"1","Pixel Data"); + DictEntry* newDict = DictEntry::New(GrPixel,NumPixel, + PixelVR,"1","Pixel Data"); - BinEntry *newEntry = new BinEntry(newDict); + DataEntry *newEntry = new DataEntry(newDict); + newDict->Delete(); newEntry->Copy(entry); newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); oldEntry->SetSelfArea(false); @@ -144,32 +244,8 @@ File::File( std::string const &filename ) } } } + return true; } - -/** - * \brief Constructor used when we want to generate dicom files from scratch - */ -File::File(): - Document() -{ - RLEInfo = new RLEFramesInfo; - JPEGInfo = new JPEGFragmentsInfo; - InitializeDefaultFile(); -} - -/** - * \brief Canonical destructor. - */ -File::~File () -{ - if( RLEInfo ) - delete RLEInfo; - if( JPEGInfo ) - delete JPEGInfo; -} - -//----------------------------------------------------------------------------- -// Public /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current File was properly parsed @@ -180,33 +256,58 @@ File::~File () */ bool File::IsReadable() { - if( !Document::IsReadable() ) + if ( !Document::IsReadable() ) { return false; } - const std::string &res = GetEntryValue(0x0028, 0x0005); + const std::string &res = GetEntryString(0x0028, 0x0005); if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { + gdcmWarningMacro("Wrong Image Dimensions" << res); return false; // Image Dimensions } + bool b0028_0100 = true; if ( !GetDocEntry(0x0028, 0x0100) ) { - return false; // "Bits Allocated" + gdcmWarningMacro("Bits Allocated (0028|0100) not found"); + //return false; // "Bits Allocated" + b0028_0100 = false; } + bool b0028_0101 = true; if ( !GetDocEntry(0x0028, 0x0101) ) { - return false; // "Bits Stored" + gdcmWarningMacro("Bits Stored (0028|0101) not found"); + //return false; // "Bits Stored" + b0028_0101 = false; } + bool b0028_0102 = true; if ( !GetDocEntry(0x0028, 0x0102) ) { - return false; // "High Bit" + gdcmWarningMacro("Hight Bit (0028|0102) not found"); + //return false; // "High Bit" + b0028_0102 = false; } + bool b0028_0103 = true; if ( !GetDocEntry(0x0028, 0x0103) ) { - return false; // "Pixel Representation" i.e. 'Sign' + gdcmWarningMacro("Pixel Representation (0028|0103) not found"); + //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed) + b0028_0103 = false; + } + + if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103) + { + gdcmWarningMacro("Too much mandatory Tags missing !"); + return false; } + if ( !GetDocEntry(GrPixel, NumPixel) ) + { + gdcmWarningMacro("Pixel Dicom Element " << std::hex << + GrPixel << "|" << NumPixel << "not found"); + return false; // Pixel Dicom Element not found :-( + } return true; } @@ -216,14 +317,8 @@ bool File::IsReadable() */ int File::GetImageNumber() { - // The function i atoi() takes the address of an area of memory as - // parameter and converts the string stored at that location to an integer - // using the external decimal to internal binary conversion rules. This may - // be preferable to sscanf() since atoi() is a much smaller, simpler and - // faster function. sscanf() can do all possible conversions whereas - // atoi() can only do single decimal integer conversions. - //0020 0013 IS REL Image Number - std::string strImNumber = GetEntryValue(0x0020,0x0013); + //0020 0013 : Image Number + std::string strImNumber = GetEntryString(0x0020,0x0013); if ( strImNumber != GDCM_UNFOUND ) { return atoi( strImNumber.c_str() ); @@ -237,50 +332,54 @@ int File::GetImageNumber() */ ModalityType File::GetModality() { - // 0008 0060 CS ID Modality - std::string strModality = GetEntryValue(0x0008,0x0060); + // 0008 0060 : Modality + std::string strModality = GetEntryString(0x0008,0x0060); if ( strModality != GDCM_UNFOUND ) { - if ( strModality.find("AU") < strModality.length()) return AU; - else if ( strModality.find("AS") < strModality.length()) return AS; - else if ( strModality.find("BI") < strModality.length()) return BI; - else if ( strModality.find("CF") < strModality.length()) return CF; - else if ( strModality.find("CP") < strModality.length()) return CP; - else if ( strModality.find("CR") < strModality.length()) return CR; - else if ( strModality.find("CT") < strModality.length()) return CT; - else if ( strModality.find("CS") < strModality.length()) return CS; - else if ( strModality.find("DD") < strModality.length()) return DD; - else if ( strModality.find("DF") < strModality.length()) return DF; - else if ( strModality.find("DG") < strModality.length()) return DG; - else if ( strModality.find("DM") < strModality.length()) return DM; - else if ( strModality.find("DS") < strModality.length()) return DS; - else if ( strModality.find("DX") < strModality.length()) return DX; + if ( strModality.find("AU") < strModality.length()) return AU; + else if ( strModality.find("AS") < strModality.length()) return AS; + else if ( strModality.find("BI") < strModality.length()) return BI; + else if ( strModality.find("CF") < strModality.length()) return CF; + else if ( strModality.find("CP") < strModality.length()) return CP; + else if ( strModality.find("CR") < strModality.length()) return CR; + else if ( strModality.find("CT") < strModality.length()) return CT; + else if ( strModality.find("CS") < strModality.length()) return CS; + else if ( strModality.find("DD") < strModality.length()) return DD; + else if ( strModality.find("DF") < strModality.length()) return DF; + else if ( strModality.find("DG") < strModality.length()) return DG; + else if ( strModality.find("DM") < strModality.length()) return DM; + else if ( strModality.find("DS") < strModality.length()) return DS; + else if ( strModality.find("DX") < strModality.length()) return DX; else if ( strModality.find("ECG") < strModality.length()) return ECG; else if ( strModality.find("EPS") < strModality.length()) return EPS; - else if ( strModality.find("FA") < strModality.length()) return FA; - else if ( strModality.find("FS") < strModality.length()) return FS; - else if ( strModality.find("HC") < strModality.length()) return HC; - else if ( strModality.find("HD") < strModality.length()) return HD; - else if ( strModality.find("LP") < strModality.length()) return LP; - else if ( strModality.find("LS") < strModality.length()) return LS; - else if ( strModality.find("MA") < strModality.length()) return MA; - else if ( strModality.find("MR") < strModality.length()) return MR; - else if ( strModality.find("NM") < strModality.length()) return NM; - else if ( strModality.find("OT") < strModality.length()) return OT; - else if ( strModality.find("PT") < strModality.length()) return PT; - else if ( strModality.find("RF") < strModality.length()) return RF; - else if ( strModality.find("RG") < strModality.length()) return RG; - else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE; - else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE; - else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN; - else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT; - else if ( strModality.find("SM") < strModality.length()) return SM; - else if ( strModality.find("ST") < strModality.length()) return ST; - else if ( strModality.find("TG") < strModality.length()) return TG; - else if ( strModality.find("US") < strModality.length()) return US; - else if ( strModality.find("VF") < strModality.length()) return VF; - else if ( strModality.find("XA") < strModality.length()) return XA; - else if ( strModality.find("XC") < strModality.length()) return XC; + else if ( strModality.find("FA") < strModality.length()) return FA; + else if ( strModality.find("FS") < strModality.length()) return FS; + else if ( strModality.find("HC") < strModality.length()) return HC; + else if ( strModality.find("HD") < strModality.length()) return HD; + else if ( strModality.find("LP") < strModality.length()) return LP; + else if ( strModality.find("LS") < strModality.length()) return LS; + else if ( strModality.find("MA") < strModality.length()) return MA; + else if ( strModality.find("MR") < strModality.length()) return MR; + else if ( strModality.find("NM") < strModality.length()) return NM; + else if ( strModality.find("OT") < strModality.length()) return OT; + else if ( strModality.find("PT") < strModality.length()) return PT; + else if ( strModality.find("RF") < strModality.length()) return RF; + else if ( strModality.find("RG") < strModality.length()) return RG; + else if ( strModality.find("RTDOSE") + < strModality.length()) return RTDOSE; + else if ( strModality.find("RTIMAGE") + < strModality.length()) return RTIMAGE; + else if ( strModality.find("RTPLAN") + < strModality.length()) return RTPLAN; + else if ( strModality.find("RTSTRUCT") + < strModality.length()) return RTSTRUCT; + else if ( strModality.find("SM") < strModality.length()) return SM; + else if ( strModality.find("ST") < strModality.length()) return ST; + else if ( strModality.find("TG") < strModality.length()) return TG; + else if ( strModality.find("US") < strModality.length()) return US; + else if ( strModality.find("VF") < strModality.length()) return VF; + else if ( strModality.find("XA") < strModality.length()) return XA; + else if ( strModality.find("XC") < strModality.length()) return XC; else { @@ -289,7 +388,6 @@ ModalityType File::GetModality() return Unknow; } } - return Unknow; } @@ -300,13 +398,10 @@ ModalityType File::GetModality() */ int File::GetXSize() { - const std::string &strSize = GetEntryValue(0x0028,0x0011); - if ( strSize == GDCM_UNFOUND ) - { - return 0; - } - - return atoi( strSize.c_str() ); + DataEntry *entry = GetDataEntry(0x0028,0x0011); + if( entry ) + return (int)entry->GetValue(0); + return 0; } /** @@ -317,18 +412,18 @@ int File::GetXSize() */ int File::GetYSize() { - const std::string &strSize = GetEntryValue(0x0028,0x0010); - if ( strSize != GDCM_UNFOUND ) - { - return atoi( strSize.c_str() ); - } + DataEntry *entry = GetDataEntry(0x0028,0x0010); + if( entry ) + return (int)entry->GetValue(0); + if ( IsDicomV3() ) { return 0; } - // The Rows (0028,0010) entry was optional for ACR/NEMA. It might - // hence be a signal (1D image). So we default to 1: + // The Rows (0028,0010) entry was optional for ACR/NEMA. + // (at least some images didn't have it.) + // It might hence be a signal (1D image). So we default to 1: return 1; } @@ -336,7 +431,7 @@ int File::GetYSize() * \brief Retrieve the number of planes of volume or the number * of frames of a multiframe. * \warning When present we consider the "Number of Frames" as the third - * dimension. When Missing we consider the third dimension as + * dimension. When missing we consider the third dimension as * being the ACR-NEMA "Planes" tag content. * @return The encountered size when found, 1 by default (single image). */ @@ -344,96 +439,112 @@ int File::GetZSize() { // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. - const std::string &strSize = GetEntryValue(0x0028,0x0008); - if ( strSize != GDCM_UNFOUND ) - { - return atoi( strSize.c_str() ); - } + DataEntry *entry = GetDataEntry(0x0028,0x0008); + if( entry ) + return (int)entry->GetValue(0); // We then consider the "Planes" entry as the third dimension - const std::string &strSize2 = GetEntryValue(0x0028,0x0012); - if ( strSize2 != GDCM_UNFOUND ) - { - return atoi( strSize2.c_str() ); - } - + entry = GetDataEntry(0x0028,0x0012); + if( entry ) + return (int)entry->GetValue(0); return 1; } /** - * \brief gets the info from 0028,0030 : Pixel Spacing + * \brief gets the info from 0018,1164 : ImagerPixelSpacing + * then 0028,0030 : Pixel Spacing * else 1.0 * @return X dimension of a pixel */ float File::GetXSpacing() { - float xspacing, yspacing; - const std::string &strSpacing = GetEntryValue(0x0028,0x0030); + float xspacing = 1.0; + uint32_t nbValue; - if( strSpacing == GDCM_UNFOUND ) - { - gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); - return 1.; - } + // To follow David Clunie's advice, we first check ImagerPixelSpacing - int nbValues; - if( ( nbValues = sscanf( strSpacing.c_str(), - "%f\\%f", &yspacing, &xspacing)) != 2 ) + DataEntry *entry = GetDataEntry(0x0018,0x1164); + if( entry ) { - // 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; + nbValue = entry->GetValueCount(); + // Can't use IsValueCountValid because of the complex heuristic. + if( nbValue >= 3 ) + xspacing = (float)entry->GetValue(2); + if( nbValue >= 2 ) + xspacing = (float)entry->GetValue(1); + else + xspacing = (float)entry->GetValue(0); if ( xspacing == 0.0 ) xspacing = 1.0; - return xspacing; - + } + else + { + gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); } - // to avoid troubles with David Clunie's-like images - if ( xspacing == 0. && yspacing == 0.) - return 1.; + entry = GetDataEntry(0x0028,0x0030); + if( entry ) + { + nbValue = entry->GetValueCount(); + if( nbValue >= 3 ) + xspacing = (float)entry->GetValue(2); + if( nbValue >= 2 ) + xspacing = (float)entry->GetValue(1); + else + xspacing = (float)entry->GetValue(0); - if ( xspacing == 0.) + if ( xspacing == 0.0 ) + xspacing = 1.0; + return xspacing; + } + else { - gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm problem"); - // seems to be a bug in the header ... - nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); - gdcmAssertMacro( nbValues == 2 ); + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } return xspacing; } /** - * \brief gets the info from 0028,0030 : Pixel Spacing + * \brief gets the info from 0018,1164 : ImagerPixelSpacing + * then from 0028,0030 : Pixel Spacing * else 1.0 * @return Y dimension of a pixel */ float File::GetYSpacing() { - float yspacing = 1.; - std::string strSpacing = GetEntryValue(0x0028,0x0030); - - if ( strSpacing == GDCM_UNFOUND ) + float yspacing = 1.0; + // To follow David Clunie's advice, we first check ImagerPixelSpacing + + DataEntry *entry = GetDataEntry(0x0018,0x1164); + if( entry ) { - gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)"); - return 1.; - } + yspacing = (float)entry->GetValue(0); - // if sscanf cannot read any float value, it won't affect yspacing - int nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing); + if ( yspacing == 0.0 ) + yspacing = 1.0; + return yspacing; + } + else + { + gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); + } - // if no values, xspacing is set to 1.0 - if( nbValues == 0 ) - yspacing = 1.0; + entry = GetDataEntry(0x0028,0x0030); + if( entry ) + { + yspacing = (float)entry->GetValue(0); - if ( yspacing == 0.0 ) - yspacing = 1.0; + if ( yspacing == 0.0 ) + yspacing = 1.0; + return yspacing; + } + else + { + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); + } return yspacing; } @@ -446,38 +557,55 @@ float File::GetYSpacing() */ float File::GetZSpacing() { - // Spacing Between Slices : distance entre le milieu de chaque coupe - // Les coupes peuvent etre : + // ---> + // ---> 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; + + // Spacing Between Slices : distance between the middle of 2 slices + // Slices may be : // jointives (Spacing between Slices = Slice Thickness) - // chevauchantes (Spacing between Slices < Slice Thickness) + // overlapping (Spacing between Slices < Slice Thickness) // disjointes (Spacing between Slices > Slice Thickness) // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal - // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ... - // Si le Spacing Between Slices est Missing, - // on suppose que les coupes sont jointives - - const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088); - - if ( strSpacingBSlices == GDCM_UNFOUND ) + // It only concerns the MRI guys, not people wanting to visualize volumes + // If Spacing Between Slices is missing, + // we suppose slices joint together + DataEntry *entry = GetDataEntry(0x0018,0x0088); + if( entry ) { + zspacing = (float)entry->GetValue(0); + + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; + } + else gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); - const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050); - if ( strSliceThickness == GDCM_UNFOUND ) - { - gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); - return 1.; - } - 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() ); - } + + // 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 ) + { + zspacing = (float)entry->GetValue(0); + + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; } - //else - return (float)atof( strSpacingBSlices.c_str() ); + else + gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); + + return zspacing; } /** @@ -488,26 +616,24 @@ float File::GetZSpacing() */ float File::GetXOrigin() { - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); - - if ( strImPos == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( !entry ) { gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); - strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos == GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x0030); + if( !entry ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); - return 0.; + return 0.0f; } } - if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + if( entry->GetValueCount() == 3 ) { - return 0.; + gdcmAssertMacro( entry->IsValueCountValid() ); + return (float)entry->GetValue(0); } - - return xImPos; + return 0.0f; } /** @@ -518,26 +644,24 @@ float File::GetXOrigin() */ float File::GetYOrigin() { - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); - - if ( strImPos == GDCM_UNFOUND) + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( !entry ) { gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); - strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos == GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x0030); + if( !entry ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); - return 0.; - } + return 0.0f; + } } - if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + if( entry->GetValueCount() == 3 ) { - return 0.; + gdcmAssertMacro( entry->IsValueCountValid() ); + return (float)entry->GetValue(1); } - - return yImPos; + return 0.0f; } /** @@ -550,101 +674,95 @@ float File::GetYOrigin() */ float File::GetZOrigin() { - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); - - if ( strImPos != GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( entry ) { - 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 + if( entry->GetValueCount() == 3 ) { - return zImPos; + gdcmAssertMacro( entry->IsValueCountValid() ); + return (float)entry->GetValue(2); } + gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); + return 0.0f; } - strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos != GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x0030); + if( entry ) { - 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 + if( entry->GetValueCount() == 3 ) { - return zImPos; + gdcmAssertMacro( entry->IsValueCountValid() ); + return (float)entry->GetValue(2); } + gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); + return 0.0f; } - std::string strSliceLocation = GetEntryValue(0x0020,0x1041); // for *very* old ACR-NEMA images - if ( strSliceLocation != GDCM_UNFOUND ) + // for *very* old ACR-NEMA images + entry = GetDataEntry(0x0020,0x1041); + if( entry ) { - if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) + if( entry->GetValueCount() == 1 ) { - gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); - return 0.; // bug in the element 0x0020,0x1041 - } - else - { - return zImPos; + gdcmAssertMacro( entry->IsValueCountValid() ); + return (float)entry->GetValue(0); // VM=1 ! } + gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); + return 0.0f; } - gdcmWarningMacro( "Unfound Slice Location (0020,1041)"); - std::string strLocation = GetEntryValue(0x0020,0x0050); - if ( strLocation != GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x0050); + if( entry ) { - if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1) - { - gdcmWarningMacro( "Wrong Location (0020,0050)"); - return 0.; // bug in the element 0x0020,0x0050 - } - else + if( entry->GetValueCount() == 1 ) { - return zImPos; + gdcmAssertMacro( entry->IsValueCountValid() ); + return (float)entry->GetValue(0); } + gdcmWarningMacro( "Wrong Location (0020,0050)"); + return 0.0f; } - 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 aray to receive values - * @return cosines of image orientation patient + * @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 */ -void File::GetImageOrientationPatient( float iop[6] ) +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.; // 0020 0037 DS REL Image Orientation (Patient) - if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND ) + if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND ) { - if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { - gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." ); + gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)." + << " Less than 6 values were found." ); + return false; } } //For ACR-NEMA // 0020 0035 DS REL Image Orientation (RET) - else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND ) + else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND ) { - if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { - gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." ); + gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). " + << "Less than 6 values were found." ); + return false; } } + return true; } /** @@ -655,67 +773,65 @@ void File::GetImageOrientationPatient( float iop[6] ) */ int File::GetBitsStored() { - std::string strSize = GetEntryValue( 0x0028, 0x0101 ); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0101); + if( !entry ) { gdcmWarningMacro("(0028,0101) is supposed to be mandatory"); - return 0; // It's supposed to be mandatory - // the caller will have to check + return 0; } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** * \brief Retrieve the number of Bits Allocated - * (8, 12 -compacted ACR-NEMA files, 16, ...) - * @return The encountered number of Bits Allocated, 0 by default. + * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,) + * @return The encountered Number of Bits Allocated, 0 by default. * 0 means the file is NOT USABLE. The caller has to check it ! */ int File::GetBitsAllocated() { - std::string strSize = GetEntryValue(0x0028,0x0100); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0100); + if( !entry ) { - gdcmWarningMacro( "(0028,0100) is supposed to be mandatory"); - return 0; // It's supposed to be mandatory - // the caller will have to check + gdcmWarningMacro("(0028,0100) is supposed to be mandatory"); + return 0; } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** * \brief Retrieve the high bit position. - * \warning The method defaults to 0 when information is Missing. + * \warning The method defaults to 0 when information is missing. * The responsability of checking this value is left to the caller. - * @return The high bit positin when present. 0 when Missing. + * @return The high bit position when present. 0 when missing. */ int File::GetHighBitPosition() { - std::string strSize = GetEntryValue( 0x0028, 0x0102 ); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0102); + if( !entry ) { - gdcmWarningMacro( "(0028,0102) is supposed to be mandatory"); + gdcmWarningMacro("(0028,0102) is supposed to be mandatory"); return 0; } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** * \brief Retrieve the number of Samples Per Pixel - * (1 : gray level, 3 : RGB -1 or 3 Planes-) + * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-) * @return The encountered number of Samples Per Pixel, 1 by default. - * (Gray level Pixels) + * (we assume Gray level Pixels) */ int File::GetSamplesPerPixel() { - const std::string &strSize = GetEntryValue(0x0028,0x0002); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0002); + if( !entry ) { - gdcmWarningMacro( "(0028,0002) is supposed to be mandatory"); + 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() ); + return (int)entry->GetValue(0); } /** @@ -725,13 +841,13 @@ int File::GetSamplesPerPixel() */ int File::GetPlanarConfiguration() { - std::string strSize = GetEntryValue(0x0028,0x0006); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0006); + if( !entry ) { gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); return 0; } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** @@ -742,9 +858,8 @@ int File::GetPlanarConfiguration() int File::GetPixelSize() { // 0028 0100 US IMG Bits Allocated - // (in order no to be messed up by old RGB images) - // if (File::GetEntryValue(0x0028,0x0100) == "24") - // return 3; + // (in order no to be messed up by old ACR-NEMA RGB images) + assert( !(GetEntryString(0x0028,0x0100) == "24") ); std::string pixelType = GetPixelType(); if ( pixelType == "8U" || pixelType == "8S" ) @@ -763,7 +878,7 @@ int File::GetPixelSize() { return 8; } - gdcmWarningMacro( "Unknown pixel type"); + gdcmWarningMacro( "Unknown pixel type: " << pixelType); return 0; } @@ -778,12 +893,13 @@ int File::GetPixelSize() * - 32S signed 32 bit, * - FD floating double 64 bits (Not kosher DICOM, but so usefull!) * \warning 12 bit images appear as 16 bit. - * 24 bit images appear as 8 bit + * 24 bit images appear as 8 bit + photochromatic interp ="RGB " + * + Planar Configuration = 0 * @return 0S if nothing found. NOT USABLE file. The caller has to check */ std::string File::GetPixelType() { - std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated + std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { gdcmWarningMacro( "Missing Bits Allocated (0028,0100)"); @@ -801,58 +917,49 @@ std::string File::GetPixelType() } else if ( bitsAlloc == "24" ) { - // (in order no to be messed up - bitsAlloc = "8"; // by old RGB images) + // (in order no to be messed up by old RGB images) + bitsAlloc = "8"; } - std::string sign = GetEntryValue(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 - } - else if ( sign == "0" ) - { - sign = "U"; + sign = "S"; } else { - sign = "S"; + sign = "U"; } return bitsAlloc + sign; } /** - * \brief Check whether the pixels are signed or UNsigned data. - * \warning The method defaults to false (UNsigned) when information is Missing. - * The responsability of checking this value is left to the caller. + * \brief Check whether the pixels are signed (1) or UNsigned (0) data. + * \warning The method defaults to false (UNsigned) when tag 0028|0103 + * is missing. + * The responsability of checking this value is left to the caller + * (NO transformation is performed on the pixels to make then >0) * @return True when signed, false when UNsigned */ bool File::IsSignedPixelData() { - std::string strSize = GetEntryValue( 0x0028, 0x0103 ); - if ( strSize == GDCM_UNFOUND ) - { - gdcmWarningMacro( "(0028,0103) is supposed to be mandatory"); - return false; - } - int sign = atoi( strSize.c_str() ); - if ( sign == 0 ) + DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation" + if( !entry ) { + gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); return false; } - return true; + return entry->GetValue(0) != 0; } /** - * \brief Check whether this a monochrome picture or not by accessing - * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * \brief Check whether this a monochrome picture (gray levels) or not, + * using "Photometric Interpretation" tag (0x0028,0x0004). * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise. */ bool File::IsMonochrome() { - const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) { @@ -865,6 +972,25 @@ bool File::IsMonochrome() return false; } +/** + * \brief Check whether this a MONOCHROME1 picture (high values = dark) + * or not using "Photometric Interpretation" tag (0x0028,0x0004). + * @return true when "MONOCHROME1" . False otherwise. + */ +bool File::IsMonochrome1() +{ + const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); + } + return false; +} + /** * \brief Check whether this a "PALETTE COLOR" picture or not by accessing * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). @@ -872,7 +998,7 @@ bool File::IsMonochrome() */ bool File::IsPaletteColor() { - std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "PALETTE COLOR " ) { return true; @@ -891,7 +1017,7 @@ bool File::IsPaletteColor() */ bool File::IsYBRFull() { - std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "YBR_FULL" ) { return true; @@ -965,7 +1091,7 @@ int File::GetLUTNbits() //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red // = Lookup Table Desc-Blue // Consistency already checked in GetLUTLength - std::string lutDescription = GetEntryValue(0x0028,0x1101); + std::string lutDescription = GetEntryString(0x0028,0x1101); if ( lutDescription == GDCM_UNFOUND ) { return 0; @@ -988,19 +1114,15 @@ int File::GetLUTNbits() */ float File::GetRescaleIntercept() { - float resInter = 0.; - /// 0028 1052 DS IMG Rescale Intercept - const std::string &strRescInter = GetEntryValue(0x0028,0x1052); - if ( strRescInter != GDCM_UNFOUND ) + // 0028 1052 DS IMG Rescale Intercept + DataEntry *entry = GetDataEntry(0x0028, 0x1052); + if( !entry ) { - if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) - { - // bug in the element 0x0028,0x1052 - gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." ); - } + gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)"); + return 0.0f; } + return (float)entry->GetValue(0); - return resInter; } /** @@ -1009,19 +1131,14 @@ float File::GetRescaleIntercept() */ float File::GetRescaleSlope() { - float resSlope = 1.; - //0028 1053 DS IMG Rescale Slope - std::string strRescSlope = GetEntryValue(0x0028,0x1053); - if ( strRescSlope != GDCM_UNFOUND ) + // 0028 1053 DS IMG Rescale Slope + DataEntry *entry = GetDataEntry(0x0028, 0x1053); + if( !entry ) { - if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) - { - // bug in the element 0x0028,0x1053 - gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); - } + gdcmWarningMacro( "Missing Rescale Slope (0028,1053)"); + return 1.0f; } - - return resSlope; + return (float)entry->GetValue(0); } /** @@ -1029,7 +1146,7 @@ float File::GetRescaleSlope() * to have to manage a LUT and expects to get an RBG Pixel image * (or a monochrome one ...) * \warning to be used with GetImagePixels() - * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) + * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*) */ int File::GetNumberOfScalarComponents() { @@ -1037,15 +1154,15 @@ int File::GetNumberOfScalarComponents() { return 3; } - + // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - if ( GetEntryValue(0x0028,0x0100) == "24" ) + if ( GetEntryString(0x0028,0x0100) == "24" ) { return 3; } - - std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004); + + std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004); if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) { @@ -1085,7 +1202,7 @@ int File::GetNumberOfScalarComponentsRaw() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - if ( File::GetEntryValue(0x0028,0x0100) == "24" ) + if ( File::GetEntryString(0x0028,0x0100) == "24" ) { return 3; } @@ -1138,17 +1255,18 @@ size_t File::GetPixelAreaLength() /** * \brief Adds the characteristics of a new element we want to anonymize - * + * @param group Group number of the target tag. + * @param elem Element number of the target tag. + * @param value new value (string) to substitute with */ 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; - AnonymizeList.push_back(el); + UserAnonymizeList.push_back(el); } /** @@ -1158,86 +1276,78 @@ void File::AddAnonymizeElement (uint16_t group, uint16_t elem, void File::AnonymizeNoLoad() { std::fstream *fp = new std::fstream(Filename.c_str(), - std::ios::in | std::ios::out | std::ios::binary); - - // TODO : FIXME - // how to white out disk space if longer than 50 ? - char spaces[50] = " "; - + std::ios::in | std::ios::out | std::ios::binary); gdcm::DocEntry *d; uint32_t offset; uint32_t lgth; - uint32_t lgtToWrite; - for (ListElements::iterator it = AnonymizeList.begin(); - it != AnonymizeList.end(); + uint32_t valLgth = 0; + std::string *spaces; + for (ListElements::iterator it = UserAnonymizeList.begin(); + it != UserAnonymizeList.end(); ++it) { - d = GetDocEntry( (*it).Group, (*it).Elem); + d = GetDocEntry( (*it).Group, (*it).Elem); if ( d == NULL) continue; - if ( dynamic_cast(d) - || dynamic_cast(d) ) + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); continue; + } offset = d->GetOffset(); lgth = d->GetLength(); - fp->seekp( offset, std::ios::beg ); - - if ( (*it).Value == "" ) + if (valLgth < lgth) { - lgtToWrite = lgth > 50 ? 50 : lgth; - fp->write( spaces, lgtToWrite ); - } - else - { - // TODO : FIXME - // how to white out disk space if longer than 50 ? - (*it).Value = (*it).Value + spaces; - lgtToWrite = lgth > (*it).Value.length() ? (*it).Value.length() : lgth; - fp->write( (char *)(*it).Value.c_str(), lgtToWrite ); - + spaces = new std::string( lgth-valLgth, ' '); + (*it).Value = (*it).Value + *spaces; + delete spaces; } + fp->seekp( offset, std::ios::beg ); + fp->write( (*it).Value.c_str(), lgth ); + } fp->close(); delete fp; } /** - * \brief anonymize a File (removes Patient's personal info passed with + * \brief anonymize a File (remove Patient's personal info passed with * AddAnonymizeElement() + * \note You cannot Anonymize a DataEntry (to be fixed) */ bool File::AnonymizeFile() { - // If Anonymisation list is empty, let's perform some basic anonymisation - if ( AnonymizeList.begin() == AnonymizeList.end() ) + // If Anonymisation list is empty, let's perform some basic anonymization + if ( UserAnonymizeList.begin() == UserAnonymizeList.end() ) { // If exist, replace by spaces - SetValEntry (" ",0x0010, 0x2154); // Telephone - SetValEntry (" ",0x0010, 0x1040); // Adress - SetValEntry (" ",0x0010, 0x0020); // Patient ID + SetEntryString(" ",0x0010, 0x2154); // Telephone + SetEntryString(" ",0x0010, 0x1040); // Adress + SetEntryString(" ",0x0010, 0x0020); // Patient ID - DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010); + DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010); if ( patientNameHE ) // we replace it by Study Instance UID (why not ?) { - std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d); + std::string studyInstanceUID = GetEntryString (0x0020, 0x000d); if ( studyInstanceUID != GDCM_UNFOUND ) { - SetValEntry(studyInstanceUID, 0x0010, 0x0010); + SetEntryString(studyInstanceUID, 0x0010, 0x0010); } else { - SetValEntry("anonymised", 0x0010, 0x0010); + SetEntryString("anonymized", 0x0010, 0x0010); } } } else { gdcm::DocEntry *d; - for (ListElements::iterator it = AnonymizeList.begin(); - it != AnonymizeList.end(); + for (ListElements::iterator it = UserAnonymizeList.begin(); + it != UserAnonymizeList.end(); ++it) { d = GetDocEntry( (*it).Group, (*it).Elem); @@ -1245,11 +1355,19 @@ bool File::AnonymizeFile() if ( d == NULL) continue; - if ( dynamic_cast(d) - || dynamic_cast(d) ) + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); continue; + } - SetValEntry ((*it).Value, (*it).Group, (*it).Elem); + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) "); + continue; + } + else + SetEntryString ((*it).Value, (*it).Group, (*it).Elem); } } @@ -1313,10 +1431,10 @@ bool File::AnonymizeFile() * (as opposed to 'DicomDir related') entries * then writes in a file all the (Dicom Elements) included the Pixels * @param fileName file name to write to - * @param filetype Type of the File to be written + * @param writetype type of the file to be written * (ACR, ExplicitVR, ImplicitVR) */ -bool File::Write(std::string fileName, FileType filetype) +bool File::Write(std::string fileName, FileType writetype) { std::ofstream *fp = new std::ofstream(fileName.c_str(), std::ios::out | std::ios::binary); @@ -1327,72 +1445,28 @@ bool File::Write(std::string fileName, FileType filetype) } // Entry : 0002|0000 = group length -> recalculated - ValEntry *e0002 = GetValEntry(0x0002,0x0000); - if( e0002 ) + DataEntry *e0000 = GetDataEntry(0x0002,0x0000); + if ( e0000 ) { std::ostringstream sLen; - sLen << ComputeGroup0002Length(filetype); - e0002->SetValue(sLen.str()); - } - - // Bits Allocated - if ( GetEntryValue(0x0028,0x0100) == "12") - { - SetValEntry("16", 0x0028,0x0100); - } - - 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() ); - InsertValEntry(s_lgPix,GrPixel, 0x0000); + sLen << ComputeGroup0002Length( ); + e0000->SetString(sLen.str()); } - // FIXME : should be nice if we could move it to File - // (or in future gdcmPixelData class) - - // Drop Palette Color, if necessary - if ( GetEntryValue(0x0028,0x0002).c_str()[0] == '3' ) - { - // if SamplesPerPixel = 3, sure we don't need any LUT ! - // Drop 0028|1101, 0028|1102, 0028|1103 - // Drop 0028|1201, 0028|1202, 0028|1203 - - DocEntry *e = GetDocEntry(0x0028,0x01101); - if (e) - { - RemoveEntryNoDestroy(e); - } - e = GetDocEntry(0x0028,0x1102); - if (e) - { - RemoveEntryNoDestroy(e); - } - e = GetDocEntry(0x0028,0x1103); - if (e) - { - RemoveEntryNoDestroy(e); - } - e = GetDocEntry(0x0028,0x01201); - if (e) - { - RemoveEntryNoDestroy(e); - } - e = GetDocEntry(0x0028,0x1202); - if (e) - { - RemoveEntryNoDestroy(e); - } - e = GetDocEntry(0x0028,0x1203); - if (e) - { - RemoveEntryNoDestroy(e); - } - } + // Derma?.dcm does not have it...let's remove it FIXME FIXME + 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); + } + } - Document::WriteContent(fp, filetype); + Document::WriteContent(fp, writetype); fp->close(); delete fp; @@ -1402,90 +1476,7 @@ bool File::Write(std::string fileName, FileType filetype) //----------------------------------------------------------------------------- // Protected -/** - * \brief Initialize a default DICOM File that should contain all the - * field require by other reader. DICOM standard does not - * explicitely defines those fields, heuristic has been choosen. - * This is not perfect as we are writting a CT image... - */ -void File::InitializeDefaultFile() -{ - std::string date = Util::GetCurrentDate(); - std::string time = Util::GetCurrentTime(); - std::string uid = Util::CreateUniqueUID(); - std::string uidMedia = uid; - std::string uidInst = uid; - std::string uidClass = Util::CreateUniqueUID(); - std::string uidStudy = Util::CreateUniqueUID(); - std::string uidSerie = Util::CreateUniqueUID(); - - // Meta Element Group Length - InsertValEntry("146 ", 0x0002, 0x0000); - // Media Storage SOP Class UID (CT Image Storage) - InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002); - // Media Storage SOP Instance UID - InsertValEntry(uidMedia.c_str(), 0x0002, 0x0003); - // Transfer Syntax UID (Explicit VR Little Endian) - InsertValEntry("1.2.840.10008.1.2.1 ", 0x0002, 0x0010); - // META Implementation Class UID - InsertValEntry(uidClass.c_str(), 0x0002, 0x0012); - // Source Application Entity Title - InsertValEntry("GDCM", 0x0002, 0x0016); - - // Instance Creation Date - InsertValEntry(date.c_str(), 0x0008, 0x0012); - // Instance Creation Time - InsertValEntry(time.c_str(), 0x0008, 0x0013); - // SOP Class UID - InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016); - // SOP Instance UID - InsertValEntry(uidInst.c_str(), 0x0008, 0x0018); - // Modality - InsertValEntry("CT", 0x0008, 0x0060); - // Manufacturer - InsertValEntry("GDCM", 0x0008, 0x0070); - // Institution Name - InsertValEntry("GDCM", 0x0008, 0x0080); - // Institution Address - InsertValEntry("http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081); - - // Patient's Name - InsertValEntry("GDCM", 0x0010, 0x0010); - // Patient ID - InsertValEntry("GDCMID", 0x0010, 0x0020); - - // Study Instance UID - InsertValEntry(uidStudy.c_str(), 0x0020, 0x000d); - // Series Instance UID - InsertValEntry(uidSerie.c_str(), 0x0020, 0x000e); - // StudyID - InsertValEntry("1", 0x0020, 0x0010); - // SeriesNumber - InsertValEntry("1", 0x0020, 0x0011); - - // Samples per pixel 1 or 3 - InsertValEntry("1", 0x0028, 0x0002); - // photochromatic interpretation - InsertValEntry("MONOCHROME1", 0x0028, 0x0004); - // nbRows - InsertValEntry("0", 0x0028, 0x0010); - // nbCols - InsertValEntry("0", 0x0028, 0x0011); - // BitsAllocated 8 or 12 or 16 - InsertValEntry("8", 0x0028, 0x0100); - // BitsStored <= BitsAllocated - InsertValEntry("8", 0x0028, 0x0101); - // HighBit <= BitsAllocated - 1 - InsertValEntry("7", 0x0028, 0x0102); - // Pixel Representation 0(unsigned) or 1(signed) - InsertValEntry("0", 0x0028, 0x0103); - - // default value - // Special case this is the image (not a string) - GrPixel = 0x7fe0; - NumPixel = 0x0010; - InsertBinEntry(0, 0, GrPixel, NumPixel); -} + //----------------------------------------------------------------------------- // Private @@ -1515,7 +1506,7 @@ void File::ComputeRLEInfo() // - the first item in the sequence of items before the encoded pixel // data stream shall be basic offset table item. The basic offset table // item value, however, is not required to be present" - ReadAndSkipEncapsulatedBasicOffsetTable(); + ReadEncapsulatedBasicOffsetTable(); // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G) // Loop on the individual frame[s] and store the information @@ -1525,8 +1516,24 @@ void File::ComputeRLEInfo() // - when more than one frame are present, then we are in // the case of a multi-frame image. long frameLength; - while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) ) + int i=0; + uint32_t sum = 0; + while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) { + // Since we have read the basic offset table, let's check the value were correct + // or else produce a warning: + if ( BasicOffsetTableItemValue ) + { + // If a BasicOffsetTableItemValue was read + uint32_t individualLength = BasicOffsetTableItemValue[i]; + assert( individualLength == sum ); // REMOVE that if this is a problem + if( individualLength != sum ) + { + gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" ); + } + sum += frameLength + 8; + i++; + } // Parse the RLE Header and store the corresponding RLE Segment // Offset Table information on fragments of this current Frame. // Note that the fragment pixels themselves are not loaded @@ -1546,9 +1553,9 @@ void File::ComputeRLEInfo() rleSegmentOffsetTable[k] = ReadInt32(); } - // Deduce from both the RLE Header and the frameLength the - // fragment length, and again store this info in a - // RLEFramesInfo. + // Deduce from both RLE Header and frameLength + // the fragment length, and again store this info + // in a RLEFramesInfo. long rleSegmentLength[15]; // skipping (not reading) RLE Segments if ( nbRleSegments > 1) @@ -1576,8 +1583,8 @@ void File::ComputeRLEInfo() RLEInfo->AddFrame(newFrame); } - // Make sure that at the end of the item we encounter a 'Sequence - // Delimiter Item': + // Make sure that we encounter a 'Sequence Delimiter Item' + // at the end of the item : if ( !ReadTag(0xfffe, 0xe0dd) ) { gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence"); @@ -1599,26 +1606,50 @@ void File::ComputeJPEGFragmentInfo() return; } - ReadAndSkipEncapsulatedBasicOffsetTable(); + ReadEncapsulatedBasicOffsetTable(); // Loop on the fragments[s] and store the parsed information in a // JPEGInfo. long fragmentLength; - while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) + int i=0; + uint32_t sum = 0; + while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) { - long fragmentOffset = Fp->tellg(); + // Since we have read the basic offset table, let's check the value were correct + // or else produce a warning: + // A.4 Transfer syntaxes for encapsulation of encoded pixel data: + // When the Item Value is present, the Basic Offset Table Item Value shall contain + // concatenated 32-bit unsigned integer values that are byte offsets to the first + // byte of the Item Tag of the first fragment for each frame in the Sequence of + // Items. These offsets are measured from the first byte of the first Item Tag + // following the Basic Offset Table item (See Table A.4-2). + + if ( BasicOffsetTableItemValue ) + { + // If a BasicOffsetTableItemValue was read + uint32_t individualLength = BasicOffsetTableItemValue[i]; + //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ?? + if( individualLength != sum ) + { + gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" << + individualLength << " != " << sum ); + } + sum += fragmentLength + 8; + i++; + } - // Store the collected info - JPEGFragment *newFragment = new JPEGFragment; - newFragment->SetOffset(fragmentOffset); - newFragment->SetLength(fragmentLength); - JPEGInfo->AddFragment(newFragment); + long fragmentOffset = Fp->tellg(); + // Store the collected info + JPEGFragment *newFragment = new JPEGFragment; + newFragment->SetOffset(fragmentOffset); + newFragment->SetLength(fragmentLength); + JPEGInfo->AddFragment(newFragment); - SkipBytes(fragmentLength); + SkipBytes(fragmentLength); } - // Make sure that at the end of the item we encounter a 'Sequence - // Delimiter Item': + // Make sure that we encounter a 'Sequence Delimiter Item' + // at the end of the item : if ( !ReadTag(0xfffe, 0xe0dd) ) { gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence"); @@ -1628,17 +1659,17 @@ void File::ComputeJPEGFragmentInfo() /** * \brief Assuming the internal file pointer \ref Document::Fp * is placed at the beginning of a tag check whether this - * tag is (TestGroup, TestElement). + * tag is (TestGroup, TestElem). * \warning On success the internal file pointer \ref Document::Fp * is modified to point after the tag. * On failure (i.e. when the tag wasn't the expected tag - * (TestGroup, TestElement) the internal file pointer + * (TestGroup, TestElem) the internal file pointer * \ref Document::Fp is restored to it's original position. - * @param testGroup The expected group of the tag. - * @param testElement The expected Element of the tag. + * @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 testElement) +bool File::ReadTag(uint16_t testGroup, uint16_t testElem) { long positionOnEntry = Fp->tellg(); long currentPosition = Fp->tellg(); // On debugging purposes @@ -1646,25 +1677,30 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElement) // Read the Item Tag group and element, and make // sure they are what we expected: uint16_t itemTagGroup; - uint16_t itemTagElement; + uint16_t itemTagElem; try { - itemTagGroup = ReadInt16(); - itemTagElement = ReadInt16(); + 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 || itemTagElement != testElement ) + if ( itemTagGroup != testGroup || itemTagElem != testElem ) { - gdcmWarningMacro( "Wrong Item Tag found:" + gdcmErrorMacro( "Wrong Item Tag found:" << " We should have found tag (" - << std::hex << testGroup << "," << testElement << ")" << std::endl + << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl << " but instead we encountered tag (" - << std::hex << itemTagGroup << "," << itemTagElement << ")" - << " at address: " << " 0x(" << (unsigned int)currentPosition << ")" + << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")" + << " at address: " << " 0x(" << std::hex + << (unsigned int)currentPosition << std::dec << ")" ) ; Fp->seekg(positionOnEntry, std::ios::beg); @@ -1682,27 +1718,27 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElement) * 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. - * @param testGroup The expected group of the tag. - * @param testElement The expected Element of the tag. + * @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 * returns 0. */ -uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElement) +uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) { - if ( !ReadTag(testGroup, testElement) ) + if ( !ReadTag(testGroup, testElem) ) { + gdcmErrorMacro( "ReadTag did not succeed for (" + << DictEntry::TranslateToKey(testGroup,testElem) + << ")..." ); return 0; } //// Then read the associated Item Length long currentPosition = Fp->tellg(); uint32_t itemLength = ReadInt32(); - { - gdcmWarningMacro( "Basic Item Length is: " - << itemLength << std::endl + gdcmDebugMacro( "Basic Item Length is: " << itemLength << " at address: " << std::hex << (unsigned int)currentPosition); - } return itemLength; } @@ -1710,7 +1746,7 @@ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElement) * \brief When parsing the Pixel Data of an encapsulated file, read * the basic offset table (when present, and BTW dump it). */ -void File::ReadAndSkipEncapsulatedBasicOffsetTable() +void File::ReadEncapsulatedBasicOffsetTable() { //// Read the Basic Offset Table Item Tag length... uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); @@ -1723,23 +1759,66 @@ void File::ReadAndSkipEncapsulatedBasicOffsetTable() // lengths, but we won't bother with such fuses for the time being. if ( itemLength != 0 ) { - char *basicOffsetTableItemValue = new char[itemLength + 1]; - Fp->read(basicOffsetTableItemValue, itemLength); + char *charBasicOffsetTableItemValue = new char[itemLength]; + Fp->read(charBasicOffsetTableItemValue, itemLength); + unsigned int nbEntries = itemLength/4; + assert( nbEntries*4 == itemLength); // Make sure this is a multiple + BasicOffsetTableItemValue = new uint32_t[nbEntries]; -#ifdef GDCM_DEBUG - for (unsigned int i=0; i < itemLength; i += 4 ) + for (unsigned int i=0; i < nbEntries; i++ ) { - uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], - uint32_t); - gdcmWarningMacro( "Read one length: " << - std::hex << individualLength ); + BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i])); +#if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION) + uint32_t val = BasicOffsetTableItemValue[i]; + BasicOffsetTableItemValue[i] + = ( (val<<24) | ((val<<8) & 0x00ff0000) | + ((val>>8) & 0x0000ff00) | (val>>24) ); +#endif + gdcmWarningMacro( "Read one length for: " << + std::hex << BasicOffsetTableItemValue[i] ); } -#endif //GDCM_DEBUG - delete[] basicOffsetTableItemValue; + delete[] charBasicOffsetTableItemValue; } } +// 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, + * 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", + File::Load()); + SetFileName( fileName ); + if ( ! this->Document::Load( ) ) + return false; + + return DoTheLoadingJob( ); +} +#endif + //----------------------------------------------------------------------------- // Print