X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Example%2FPrintFile.cxx;h=8e42f004dfa91d426524ca02ee106f65ef54e751;hb=17daf7e7caceddf44e73864ee8d366613a1f0c82;hp=0e780d213abf6fde248bdffcdc195cdfd94bbf1f;hpb=770d6ef4630d6243dba1813a75c3dc2f62668a8c;p=gdcm.git diff --git a/Example/PrintFile.cxx b/Example/PrintFile.cxx index 0e780d21..8e42f004 100644 --- a/Example/PrintFile.cxx +++ b/Example/PrintFile.cxx @@ -1,88 +1,600 @@ +/*========================================================================= + + Program: gdcm + Module: $RCSfile: PrintFile.cxx,v $ + Language: C++ + Date: $Date: 2005/11/28 11:54:45 $ + Version: $Revision: 1.75 $ + + 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 -#include "gdcm.h" -int main(int argc, char* argv[]) +// TODO : code factorization, for 'single file' an 'whole directory' processing + +void ShowLutData(gdcm::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::File *f) +{ + gdcm::SeqEntry *modLutSeq = f->GetSeqEntry(0x0028,0x3000); + if ( modLutSeq !=0 ) + { + gdcm::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::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[]) { - - gdcmHeader *e1; - gdcmFile *f1; - std::string fileName; - if (argc != 2) { - std::cout << " usage : PrintDocument fileName" << std::endl; + + 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] ", + " [dict= privateDirectory] ", + " [ { [noshadowseq] | [noshadow][noseq] } ] ", + " [debug] [warning] ", + " level = 0,1,2 : depending on the amount of details user wants to see", + " 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::ArgMgr *am= new gdcm::ArgMgr(argc, argv); + + if (argc == 1 || am->ArgMgrDefined("usage") ) + { + am->ArgMgrUsage(usage); // Display 'usage' + delete am; + return 1; } - if (argc > 1) { - fileName=argv[1]; - } else { - fileName += GDCM_DATA_ROOT; - fileName += "/test.acr"; + char *fileName = am->ArgMgrGetString("filein",(char *)0); + char *dirName = am->ArgMgrGetString("dirin",(char *)0); + + 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; } - - e1= new gdcmHeader( fileName.c_str() ); - f1 = new gdcmFile(e1); + if (am->ArgMgrDefined("debug")) + gdcm::Debug::DebugOn(); - e1->SetPrintLevel(2); - - e1->Print(); + if (am->ArgMgrDefined("warning")) + gdcm::Debug::WarningOn(); + + int loadMode = gdcm::LD_ALL; + if ( am->ArgMgrDefined("noshadowseq") ) + loadMode |= gdcm::LD_NOSHADOWSEQ; + else + { + if ( am->ArgMgrDefined("noshadow") ) + loadMode |= gdcm::LD_NOSHADOW; + if ( am->ArgMgrDefined("noseq") ) + loadMode |= gdcm::LD_NOSEQ; + } + + int level = am->ArgMgrGetInt("level", 1); + + int forceLoadNb; + uint16_t *elemsToForceLoad + = am->ArgMgrGetXInt16Enum("forceload", &forceLoadNb); + + bool showlut = ( 0 != am->ArgMgrDefined("SHOWLUT") ); + + bool ddict = am->ArgMgrDefined("dict") ? true : false; + char *dict = 0; + + if (ddict) + { + dict = am->ArgMgrGetString("dict",(char *)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::Global::GetDicts()->GetDefaultPubDict()->AddDict(dict); + } + + if ( fileName != 0 ) // ====== Deal with a single file ====== + { + gdcm::File *f = gdcm::File::New(); + f->SetLoadMode(loadMode); + f->SetFileName( fileName ); + + 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 = f->Load(); + // gdcm::File::IsReadable() is no usable here, because we deal with + // any kind of gdcm-Parsable *document* + // not only gdcm::File (as opposed to gdcm::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; + } + + gdcm::FileHelper *fh = gdcm::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; + + int nX,nY,nZ,sPP,planarConfig; + std::string pixelType; + nX=f->GetXSize(); + nY=f->GetYSize(); + nZ=f->GetZSize(); + std::cout << " DIMX=" << nX << " DIMY=" << nY << " DIMZ=" << nZ + << 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; + +//------------------------------ + // Lets's get and print some usefull fields about 'Orientation' + // ------------------------------------------------------------ + + std::string strPatientPosition = + f->GetEntryString(0x0018,0x5100); + if ( strPatientPosition != gdcm::GDCM_UNFOUND + && strPatientPosition != "" ) + std::cout << "PatientPosition (0x0010,0x5100)= [" + << strPatientPosition << "]" << std::endl; + + std::string strViewPosition = + f->GetEntryString(0x0018,0x5101); + if ( strViewPosition != gdcm::GDCM_UNFOUND + && strViewPosition != "" ) + std::cout << "strViewPosition (0x0010,0x5101)= [" + << strViewPosition << "]" << std::endl; - std::cout << "\n\n" << std::endl; - - int dataSize = f1->GetImageDataSize(); - std::cout <GetXSize(); - nY=e1->GetYSize(); - nZ=e1->GetZSize(); - std::cout << " DIMX=" << nX << " DIMY=" << nY << " DIMZ=" << nZ << std::endl; - - pixelType = e1->GetPixelType(); - sPP = e1->GetSamplesPerPixel(); - planarConfig = e1->GetPlanarConfiguration(); - - std::cout << " pixelType=" << pixelType - << " SampleserPixel=" << sPP - << " PlanarConfiguration=" << planarConfig - << std::endl - << " PhotometricInterpretation=" - << e1->GetEntryByNumber(0x0028,0x0004) - << std::endl; + std::string strPatientOrientation = + f->GetEntryString(0x0020,0x0020); + if ( strPatientOrientation != gdcm::GDCM_UNFOUND + && strPatientOrientation != "") + std::cout << "PatientOrientation (0x0020,0x0020)= [" + << strPatientOrientation << "]" << std::endl; + + std::string strImageOrientationPatient = + f->GetEntryString(0x0020,0x0037); + if ( strImageOrientationPatient != gdcm::GDCM_UNFOUND + && strImageOrientationPatient != "" ) + std::cout << "ImageOrientationPatient (0x0020,0x0037)= [" + << strImageOrientationPatient << "]" << std::endl; - int numberOfScalarComponents=e1->GetNumberOfScalarComponents(); - std::cout << " NumberOfScalarComponents " << numberOfScalarComponents <GetEntryString(0x0020,0x0035); + if ( strImageOrientationRET != gdcm::GDCM_UNFOUND + && strImageOrientationRET != "" ) + std::cout << "ImageOrientationRET (0x0020,0x0035)= [" + << strImageOrientationRET << "]" << std::endl; + // Let's compute 'user friendly' results about 'Orientation' + // --------------------------------------------------------- + + gdcm::Orientation *o = gdcm::Orientation::New(); + + if ( strImageOrientationPatient != gdcm::GDCM_UNFOUND || + strImageOrientationRET != gdcm::GDCM_UNFOUND ) + { - if ( e1->GetEntryByNumber(0x0002,0x0010) == GDCM_NOTLOADED ) { - std::cout << "Transfert Syntax not loaded. " << std::endl - << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" - << std::endl; - return 0; - } + gdcm::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->gdcm::Orientation::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 - std::string transferSyntaxName = e1->GetTransfertSyntaxName(); - std::cout << " TransferSyntaxName= [" << transferSyntaxName << "]" << std::endl; - - if ( transferSyntaxName != "Implicit VR - Little Endian" - && transferSyntaxName != "Explicit VR - Little Endian" - && transferSyntaxName != "Deflated Explicit VR - Little Endian" - && transferSyntaxName != "Explicit VR - Big Endian" - && transferSyntaxName != "Uncompressed ACR-NEMA" ) - { - std::cout << std::endl << "===========================================" - << std::endl; - f1->ParsePixelData(); - std::cout << std::endl << "===========================================" - << std::endl; - } + gdcm::SeqEntry *modLutSeq = f->GetSeqEntry(0x0028,0x3000); + if ( modLutSeq !=0 ) + { + gdcm::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::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::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::DirList dirList(dirName,1); // gets recursively the file list + gdcm::DirListType fileList = dirList.GetFilenames(); + gdcm::File *f; + bool res; + + for( gdcm::DirListType::iterator it = fileList.begin(); + it != fileList.end(); + ++it ) + { + std::cout << std::endl<<" Start processing :[" << it->c_str() << "]" + << std::endl; + f = gdcm::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::FileHelper *fh = gdcm::FileHelper::New(f); + fh->SetPrintLevel( level ); + fh->Print(); + +//------------------------------ + + // Lets's get and print some usefull fields about 'Orientation' + // ------------------------------------------------------------ + + std::string strPatientPosition = + f->GetEntryString(0x0018,0x5100); + if ( strPatientPosition != gdcm::GDCM_UNFOUND + && strPatientPosition != "" ) + std::cout << "PatientPosition (0x0010,0x5100)= [" + << strPatientPosition << "]" << std::endl; + + std::string strViewPosition = + f->GetEntryString(0x0018,0x5101); + if ( strViewPosition != gdcm::GDCM_UNFOUND + && strViewPosition != "" ) + std::cout << "strViewPosition (0x0010,0x5101)= [" + << strViewPosition << "]" << std::endl; + + std::string strPatientOrientation = + f->GetEntryString(0x0020,0x0020); + if ( strPatientOrientation != gdcm::GDCM_UNFOUND + && strPatientOrientation != "") + std::cout << "PatientOrientation (0x0020,0x0020)= [" + << strPatientOrientation << "]" << std::endl; + + std::string strImageOrientationPatient = + f->GetEntryString(0x0020,0x0037); + if ( strImageOrientationPatient != gdcm::GDCM_UNFOUND + && strImageOrientationPatient != "" ) + std::cout << "ImageOrientationPatient (0x0020,0x0037)= [" + << strImageOrientationPatient << "]" << std::endl; + + std::string strImageOrientationRET = + f->GetEntryString(0x0020,0x0035); + if ( strImageOrientationRET != gdcm::GDCM_UNFOUND + && strImageOrientationRET != "" ) + { + std::cout << "ImageOrientationRET (0x0020,0x0035)= [" + << strImageOrientationRET << "]" << std::endl; + } + + // Let's compute 'user friendly' results about 'Orientation' + // --------------------------------------------------------- + + gdcm::Orientation *o = gdcm::Orientation::New(); + + + if ( strImageOrientationPatient != gdcm::GDCM_UNFOUND || + strImageOrientationRET != gdcm::GDCM_UNFOUND ) + { + + gdcm::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; - if(e1->IsReadable()) - std::cout <gdcm::Orientation::Delete(); +//------------------------------- + + if (f->IsReadable()) + std::cout <c_str()<<" is Readable"<c_str()<<" is NOT Readable"<Delete(); + fh->Delete(); + } + std::cout<