/*========================================================================= Program: gdcm Module: $RCSfile: PrintFile.cxx,v $ Language: C++ Date: $Date: 2008/05/20 09:21:22 $ Version: $Revision: 1.91 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "gdcmFile.h" #include "gdcmDocument.h" #include "gdcmSeqEntry.h" #include "gdcmSQItem.h" #include "gdcmDataEntry.h" #include "gdcmFileHelper.h" #include "gdcmDebug.h" #include "gdcmDirList.h" #include "gdcmGlobal.h" #include "gdcmDictSet.h" #include "gdcmArgMgr.h" #include "gdcmOrientation.h" #include /// \todo : code factorization, for 'single file' an 'whole directory' processing void ShowLutData(GDCM_NAME_SPACE::File *f); // Nothing is written yet to get LUT Data user friendly // The following is to be moved into a PixelReadConvert method // Let here, waiting for a clever idea on the way to do it. void ShowLutData(GDCM_NAME_SPACE::File *f) { GDCM_NAME_SPACE::SeqEntry *modLutSeq = f->GetSeqEntry(0x0028,0x3000); if ( modLutSeq !=0 ) { GDCM_NAME_SPACE::SQItem *sqi= modLutSeq->GetFirstSQItem(); if ( sqi != 0 ) { std::string lutDescriptor = sqi->GetEntryString(0x0028,0x3002); if ( /*lutDescriptor == GDCM_UNFOUND*/ 0 ) { std::cout << "LUT Descriptor is missing" << std::endl; return; } int length; // LUT length in Bytes int deb; // Subscript of the first Lut Value int nbits; // Lut item size (in Bits) int nbRead; // nb of items in LUT descriptor (must be = 3) nbRead = sscanf( lutDescriptor.c_str(), "%d\\%d\\%d", &length, &deb, &nbits ); std::cout << "length " << length << " deb " << deb << " nbits " << nbits << std::endl; if ( nbRead != 3 ) { std::cout << "Wrong LUT descriptor" << std::endl; } //LUT Data (CTX dependent) GDCM_NAME_SPACE::DataEntry *b = sqi->GetDataEntry(0x0028,0x3006); if ( b != 0 ) { int BitsAllocated = f->GetBitsAllocated(); if ( BitsAllocated <= 8 ) { int mult; if ( ( nbits == 16 ) && ( BitsAllocated == 8 ) ) { // when LUT item size is different than pixel size mult = 2; // high byte must be = low byte } else { // See PS 3.3-2003 C.11.1.1.2 p 619 mult = 1; } uint8_t *lut = b->GetBinArea(); for( int i=0; i < length; ++i ) { std::cout << i+deb << " : \t" << (int) (lut[i*mult + 1]) << std::endl; } } else { uint16_t *lut = (uint16_t *)(b->GetBinArea()); for( int i=0; i < length; ++i ) { std::cout << i+deb << " : \t" << (int) (((uint16_t *)lut)[i]) << std::endl; } } } else std::cout << "No LUT Data DataEntry (0x0028,0x3006) found?!? " << std::endl; } else std::cout << "No First SQ Item within (0x0028,0x3000) ?!? " << std::endl; } else std::cout << "No LUT Data SeqEntry (0x0028,0x3000) found " << std::endl; } int main(int argc, char *argv[]) { START_USAGE(usage) " \n PrintFile : \n ", " Display the header of a ACR-NEMA/PAPYRUS/DICOM File ", " usage: PrintFile {filein=inputFileName|dirin=inputDirectoryName}[level=n]", " [forceload=listOfElementsToForceLoad] [rec] [noex] ", " [4DLoc= ][dict= privateDirectory] ", " [ { [noshadowseq] | [noshadow][noseq] } ] [load] ", " [debug] [warning] ", " level = 0,1,2 : depending on the amount of details user wants to see", " rec : user wants to parse recursively the directory ", " load : user wants to load the pixels, as well (to see warning info) ", " noex : user doesn't want extra 'user friendly' info ", " 4DLoc: group-elem(in hexa, no space) of the DataEntry holdind 4thDim", " listOfElementsToForceLoad : group-elem,g2-e2,... (in hexa, no space)", " of Elements to load whatever their length ", " privateDirectory : source file full path name of Shadow Group elems ", " noshadowseq: user doesn't want to load Private Sequences ", " noshadow : user doesn't want to load Private groups (odd number) ", " noseq : user doesn't want to load Sequences ", " debug : user wants to run the program in 'debug mode' ", " warning : user wants to be warned about any oddity in the File ", " showlut :user wants to display the Palette Color (as an int array) ", FINISH_USAGE // Initialize Arguments Manager GDCM_NAME_SPACE::ArgMgr *am= new GDCM_NAME_SPACE::ArgMgr(argc, argv); if (argc == 1 || am->ArgMgrDefined("usage") ) { am->ArgMgrUsage(usage); // Display 'usage' delete am; return 1; } const char *fileName = am->ArgMgrGetString("filein"); const char *dirName = am->ArgMgrGetString("dirin"); if ( (fileName == 0 && dirName == 0) || (fileName != 0 && dirName != 0) ) { std::cerr << std::endl << "Either 'filein=' or 'dirin=' must be present;" << std::endl << "Not both" << std::endl; am->ArgMgrUsage(usage); // Display 'usage' delete am; return 1; } bool noex = ( 0 != am->ArgMgrDefined("noex") ); bool rec = ( 0 != am->ArgMgrDefined("rec") ); if (am->ArgMgrDefined("debug")) GDCM_NAME_SPACE::Debug::DebugOn(); if (am->ArgMgrDefined("warning")) GDCM_NAME_SPACE::Debug::WarningOn(); int loadMode = GDCM_NAME_SPACE::LD_ALL; if ( am->ArgMgrDefined("noshadowseq") ) loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ; else { if ( am->ArgMgrDefined("noshadow") ) loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW; if ( am->ArgMgrDefined("noseq") ) loadMode |= GDCM_NAME_SPACE::LD_NOSEQ; } int level = am->ArgMgrGetInt("level", 1); int forceLoadNb; uint16_t *elemsToForceLoad = am->ArgMgrGetXInt16Enum("forceload", &forceLoadNb); int nbP =0; uint16_t *FourthDimLoc; if ( am->ArgMgrDefined("4DLoc") ) { FourthDimLoc = am->ArgMgrGetXInt16Enum("4DLoc", &nbP); if (nbP != 1) { std::cout << "4DLoc must have 2 and only 2 components!" << std::endl; delete am; return 1; } } bool load = ( 0 != am->ArgMgrDefined("load") ); bool showlut = ( 0 != am->ArgMgrDefined("SHOWLUT") ); bool ddict = am->ArgMgrDefined("dict") ? true : false; const char *dict = 0; if (ddict) { dict = am->ArgMgrGetString("dict",0); } /* if unused Param we give up */ if ( am->ArgMgrPrintUnusedLabels() ) { am->ArgMgrUsage(usage); delete am; return 1; } delete am; // we don't need Argument Manager any longer // ----------- End Arguments Manager --------- if (ddict) { GDCM_NAME_SPACE::Global::GetDicts()->GetDefaultPubDict()->AddDict(dict); } if ( fileName != 0 ) // ====== Deal with a single file ====== { GDCM_NAME_SPACE::File *f = GDCM_NAME_SPACE::File::New(); f->SetLoadMode(loadMode); f->SetFileName( fileName ); f->SetMaxSizeLoadEntry(0xffff); for (int ri=0; riAddForceLoadElement((uint32_t)elemsToForceLoad[2*ri], (uint32_t)elemsToForceLoad[2*ri+1] ); } // TODO : find why such a polution // To avoid polluting the output with messages // 'Last system error was : No such file or directory' errno = 0; bool res = false; try { res = f->Load(); } catch(std::exception &ex) { std::cerr << "sorry an exception was thrown: " << ex.what() << std::endl; } // GDCM_NAME_SPACE::File::IsReadable() is no usable here, because we deal with // any kind of gdcm-Parsable *document* // not only GDCM_NAME_SPACE::File (as opposed to GDCM_NAME_SPACE::DicomDir) if ( !res ) { std::cout << "Cannot process file [" << fileName << "]" << std::endl; std::cout << "Either it doesn't exist, or it's read protected " << std::endl; std::cout << "or it's not a Dicom File, or its 'header' is bugged" << std::endl; std::cout << "use 'PrintFile filein=... debug' to try to guess the pb" << std::endl; f->Delete(); return 0; } if (nbP == 1) f->SetFourthDimensionLocation(FourthDimLoc[0],FourthDimLoc[1]); GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(f); fh->SetPrintLevel( level ); fh->Print(); std::cout << "\n\n" << std::endl; std::cout <GetImageDataSize() << std::endl; std::cout <<" dataSizeRaw " << fh->GetImageDataRawSize() << std::endl; if (!noex) { int nX,nY,nZ,nT,sPP,planarConfig; std::string pixelType; nX=f->GetXSize(); nY=f->GetYSize(); nZ=f->GetZSize(); nT=f->GetTSize(); std::cout << " DIMX=" << nX << " DIMY=" << nY << " DIMZ=" << nZ << " DIMT=" << nT << std::endl; pixelType = f->GetPixelType(); sPP = f->GetSamplesPerPixel(); std::cout << " pixelType= [" << pixelType << "] SamplesPerPixel= [" << sPP << "] "; if (sPP == 3) { planarConfig = f->GetPlanarConfiguration(); std::cout << " PlanarConfiguration= [" << planarConfig << "] "<< std::endl; } std::cout << " PhotometricInterpretation= [" << f->GetEntryString(0x0028,0x0004) << "] "<< std::endl; int numberOfScalarComponents=f->GetNumberOfScalarComponents(); std::cout << " NumberOfScalarComponents = " << numberOfScalarComponents <GetDataEntry(0x0002,0x0010) ) if ( f->GetDataEntry(0x0002,0x0010)->IsNotLoaded() ) { std::cout << "Transfer Syntax not loaded. " << std::endl << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" << std::endl; f->Delete(); return 0; } std::string transferSyntaxName = f->GetTransferSyntaxName(); std::cout << " TransferSyntaxName= [" << transferSyntaxName << "]" << std::endl; std::cout << " SwapCode= " << f->GetSwapCode() << std::endl; std::cout << " ------" << std::endl; std::cout << "\n\n" << std::endl; std::cout << "X spacing " << f->GetXSpacing() << std::endl; std::cout << "Y spacing " << f->GetYSpacing() << std::endl; std::cout << "Z spacing " << f->GetZSpacing() << std::endl; //------------------------------ // Let's get and print some usefull fields about 'Orientation' // ------------------------------------------------------------ std::string strPatientPosition = f->GetEntryString(0x0018,0x5100); if ( strPatientPosition != GDCM_NAME_SPACE::GDCM_UNFOUND && strPatientPosition != "" ) std::cout << "PatientPosition (0x0010,0x5100)= [" << strPatientPosition << "]" << std::endl; std::string strViewPosition = f->GetEntryString(0x0018,0x5101); if ( strViewPosition != GDCM_NAME_SPACE::GDCM_UNFOUND && strViewPosition != "" ) std::cout << "View Position (0x0018,0x5101)= [" << strViewPosition << "]" << std::endl; std::string strPatientOrientation = f->GetEntryString(0x0020,0x0020); if ( strPatientOrientation != GDCM_NAME_SPACE::GDCM_UNFOUND && strPatientOrientation != "") std::cout << "PatientOrientation (0x0020,0x0020)= [" << strPatientOrientation << "]" << std::endl; std::string strImageOrientationPatient = f->GetEntryString(0x0020,0x0037); if ( strImageOrientationPatient != GDCM_NAME_SPACE::GDCM_UNFOUND && strImageOrientationPatient != "" ) std::cout << "ImageOrientationPatient (0x0020,0x0037)= [" << strImageOrientationPatient << "]" << std::endl; std::string strImageOrientationRET = f->GetEntryString(0x0020,0x0035); if ( strImageOrientationRET != GDCM_NAME_SPACE::GDCM_UNFOUND && strImageOrientationRET != "" ) std::cout << "ImageOrientationRET (0x0020,0x0035)= [" << strImageOrientationRET << "]" << std::endl; std::string strImagePositionPatient = f->GetEntryString(0x0020,0x0032); if ( strImagePositionPatient != GDCM_NAME_SPACE::GDCM_UNFOUND && strImagePositionPatient != "" ) std::cout << "ImagePositionPatient (0x0020,0x0032)= [" << strImagePositionPatient << "]" << std::endl; std::string strImagePositionPatientRET = f->GetEntryString(0x0020,0x0030); if ( strImagePositionPatientRET != GDCM_NAME_SPACE::GDCM_UNFOUND && strImagePositionPatientRET != "" ) std::cout << "ImagePositionPatientRET (0x0020,0x0030)= [" << strImagePositionPatientRET << "]" << std::endl; float iop[6]; /*bool riop = */f->GetImageOrientationPatient(iop); float ipp[3]; /*bool ripp = */f->GetImagePositionPatient(ipp); std::cout << "Image Position (0x0020,0x0032|0x0030) : " << ipp[0] << " , " << ipp[1] << " , "<< ipp[2] << std::endl; std::cout << "Image Orientation (0x0020,0x0037|0x0035) : " << iop[0] << " , " << iop[1] << " , "<< iop[2] << " , " << iop[3] << " , " << iop[4] << " , "<< iop[5] << std::endl; // Let's compute 'user friendly' results about 'Orientation' // --------------------------------------------------------- GDCM_NAME_SPACE::Orientation *o = GDCM_NAME_SPACE::Orientation::New(); if ( strImageOrientationPatient != GDCM_NAME_SPACE::GDCM_UNFOUND || strImageOrientationRET != GDCM_NAME_SPACE::GDCM_UNFOUND ) { GDCM_NAME_SPACE::OrientationType orient = o->GetOrientationType( f ); std::cout << "TypeOrientation = " << orient << " (-> " << o->GetOrientationTypeString(orient) << " )" << std::endl; } std::string ori = o->GetOrientation ( f ); if (ori != "\\" ) std::cout << "Orientation [" << ori << "]" << std::endl; o->Delete(); /* std::vector valueVector; GDCM_NAME_SPACE::DataEntry *e_0018_5212 = f->GetDataEntry(0x0018, 0x5212); bool resJP = e_0018_5212->GetDSValue(valueVector); if (resJP) { double test; for ( int i=0; i < 3; i++ ) { test = valueVector[i]; std::cout << " test " << test << std::endl; } } //e_0018_5212->Delete(); */ } //------------------------------ // Display the LUT as an int array (for debugging purpose) if ( f->HasLUT() && showlut ) { uint8_t* lutrgba = fh->GetLutRGBA(); if ( lutrgba == 0 ) { std::cout << "Lut RGBA (Palette Color) not built " << std::endl; // Nothing is written yet to get LUT Data user friendly // The following is to be moved into a PixelRedaConvert method GDCM_NAME_SPACE::SeqEntry *modLutSeq = f->GetSeqEntry(0x0028,0x3000); if ( modLutSeq !=0 ) { GDCM_NAME_SPACE::SQItem *sqi= modLutSeq->GetFirstSQItem(); if ( !sqi ) { std::string lutDescriptor = sqi->GetEntryString(0x0028,0x3002); int length; // LUT length in Bytes int deb; // Subscript of the first Lut Value int nbits; // Lut item size (in Bits) int nbRead; // nb of items in LUT descriptor (must be = 3) nbRead = sscanf( lutDescriptor.c_str(), "%d\\%d\\%d", &length, &deb, &nbits ); if ( nbRead != 3 ) { std::cout << "Wrong LUT descriptor" << std::endl; } GDCM_NAME_SPACE::DataEntry *b = sqi->GetDataEntry(0x0028,0x3006); if ( b != 0 ) { if ( b->GetLength() != 0 ) { std::cout << "---------------------------------------" << " We should never reach this point " << std::endl; //LoadEntryBinArea(b); //LUT Data (CTX dependent) } } } } else std::cout << "No LUT Data (0x0028,0x3000) found " << std::endl; } /* else { if ( fh->GetLutItemSize() == 8 ) { for (int i=0;iGetLutItemNumber();i++) std::cout << i << " : \t" << (int)(lutrgba[i*4]) << " " << (int)(lutrgba[i*4+1]) << " " << (int)(lutrgba[i*4+2]) << std::endl; } else // LutItemSize assumed to be = 16 { uint16_t* lutrgba16 = (uint16_t*)lutrgba; for (int i=0;iGetLutItemNumber();i++) std::cout << i << " : \t" << (int)(lutrgba16[i*4]) << " " << (int)(lutrgba16[i*4+1]) << " " << (int)(lutrgba16[i*4+2]) << std::endl; } } */ } else if (showlut) { std::cout << "Try LUT Data "<< std::endl; ShowLutData(f); } // Parsability of the GDCM_NAME_SPACE::Document already checked, after Load() ! if ( f->IsReadable() ) { std::cout <GetSeqEntry(0x0041,0x1010) ) { std::cout <GetSeqEntry(0x0004,0x1220) ) { std::cout <Delete(); fh->Delete(); } // =========================================================================== else // =============================== Deal with a Directory ===================== { // =========================================================================== std::cout << "dirName [" << dirName << "]" << std::endl; GDCM_NAME_SPACE::DirList dirList(dirName,rec); // gets recursively (or not) the file list GDCM_NAME_SPACE::DirListType fileList = dirList.GetFilenames(); GDCM_NAME_SPACE::File *f; bool res; if (fileList.size() == 0) { std::cout << "No file found in : [" << dirName << "]" << std::endl; } for( GDCM_NAME_SPACE::DirListType::iterator it = fileList.begin(); it != fileList.end(); ++it ) { std::cout << std::endl<<" Start processing :[" << it->c_str() << "]" << std::endl; f = GDCM_NAME_SPACE::File::New(); f->SetLoadMode(loadMode); f->SetFileName( it->c_str() ); for (int ri=0; riAddForceLoadElement((uint32_t)elemsToForceLoad[2*ri], (uint32_t)elemsToForceLoad[2*ri+1]); } res = f->Load(); if ( !res ) { std::cout << "Cannot process file [" << it->c_str() << "]" << std::endl; std::cout << "Either it doesn't exist, or it's read protected " << std::endl; std::cout << "or it's not a Dicom File, or its 'header' is bugged" << std::endl; std::cout << "use 'PrintFile filein=... debug' " << "to try to guess the pb" << std::endl; f->Delete(); continue; } GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(f); fh->SetPrintLevel( level ); fh->Print(); //------------------------------ if (!noex) { // Lets's get and print some usefull fields about 'Orientation' // ------------------------------------------------------------ std::string strPatientPosition = f->GetEntryString(0x0018,0x5100); if ( strPatientPosition != GDCM_NAME_SPACE::GDCM_UNFOUND && strPatientPosition != "" ) std::cout << "PatientPosition (0x0010,0x5100)= [" << strPatientPosition << "]" << std::endl; std::string strViewPosition = f->GetEntryString(0x0018,0x5101); if ( strViewPosition != GDCM_NAME_SPACE::GDCM_UNFOUND && strViewPosition != "" ) std::cout << "strViewPosition (0x0010,0x5101)= [" << strViewPosition << "]" << std::endl; std::string strPatientOrientation = f->GetEntryString(0x0020,0x0020); if ( strPatientOrientation != GDCM_NAME_SPACE::GDCM_UNFOUND && strPatientOrientation != "") std::cout << "PatientOrientation (0x0020,0x0020)= [" << strPatientOrientation << "]" << std::endl; std::string strImageOrientationPatient = f->GetEntryString(0x0020,0x0037); if ( strImageOrientationPatient != GDCM_NAME_SPACE::GDCM_UNFOUND && strImageOrientationPatient != "" ) std::cout << "ImageOrientationPatient (0x0020,0x0037)= [" << strImageOrientationPatient << "]" << std::endl; std::string strImageOrientationRET = f->GetEntryString(0x0020,0x0035); if ( strImageOrientationRET != GDCM_NAME_SPACE::GDCM_UNFOUND && strImageOrientationRET != "" ) { std::cout << "ImageOrientationRET (0x0020,0x0035)= [" << strImageOrientationRET << "]" << std::endl; } // Let's compute 'user friendly' results about 'Orientation' // --------------------------------------------------------- GDCM_NAME_SPACE::Orientation *o = GDCM_NAME_SPACE::Orientation::New(); if ( strImageOrientationPatient != GDCM_NAME_SPACE::GDCM_UNFOUND || strImageOrientationRET != GDCM_NAME_SPACE::GDCM_UNFOUND ) { GDCM_NAME_SPACE::OrientationType orient = o->GetOrientationType( f ); std::cout << "TypeOrientation = " << orient << " (-> " << o->GetOrientationTypeString(orient) << " )" << std::endl; } std::string ori = o->GetOrientation ( f ); if (ori != "\\" ) std::cout << "Orientation [" << ori << "]" << std::endl; o->Delete(); } //------------------------------- if (f->IsReadable()) { if (load) // just to see warning messages at load time ! { uint8_t *pixels = fh->GetImageData(); (void)pixels; uint32_t lgth = fh->GetImageDataSize(); (void)lgth; } std::cout <c_str()<<" is Readable"<c_str()<<" is NOT Readable"<Delete(); fh->Delete(); } std::cout<