/*========================================================================= Program: gdcm Module: $RCSfile: exConvert3DplusT.cxx,v $ Language: C++ Date: $Date: 2006/09/01 13:25:27 $ Version: $Revision: 1.3 $ 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. =========================================================================*/ // // This program is used to convert huge amounts of functionnal (3D + T) MR images // into 'image tiles' (one title per volume) processable by clinical softwares // #include "gdcmFile.h" #include "gdcmFileHelper.h" #include "gdcmCommon.h" #include "gdcmDebug.h" #include "gdcmDirList.h" #include "gdcmUtil.h" #include "gdcmArgMgr.h" #include #include #include // for memset int main(int argc, char *argv[]) { START_USAGE(usage) "\n exConvert3plusT :\n ", " Converts the Dicom files inside a single-level Directory ", " into a '3D + T' image set ", " usage: exConvert3plusT ", " dirin=inputDirectoryName ", " dirout=outputDirectoryName ", " [studyUID = ] [patName = ] ", " [ { [noshadowseq] | [noshadow][noseq] } ] [debug] [verbose]", " ", " dirin : single-level Directory containing the images ", " (no recursive parsing) ", " dirout : will be created if doesn't exist ", " ", " [imdimx = ] [imdimy = ] [imgline = ] [imgcol = ] ", " [pixelsize = ] [imagesinvolume = ] ", " ", " studyUID : *aware* user wants to add the serie ", " to an already existing study ", " imdimx,imdimy : 'elementary image' size (default : 64) ", " used to reject erroneous images ", " imgline, imgcol : sizes of the 'image tile' defaulted as 6x6 ", " pixelsize : in bytes; defaulted as 2 (uint16_t) ", " used to reject erroneous images ", " imagesinvolume : we have no way to guess it! ", " defaulted as imgline*imgcol ", " 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 ", " verbose : user wants to run the program in 'verbose mode' ", " debug : developper wants to run the program in 'debug mode' ", FINISH_USAGE // ----- Initialize Arguments Manager ------ gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv); if (am->ArgMgrDefined("usage") || argc == 1) { am->ArgMgrUsage(usage); // Display 'usage' delete am; return 0; } if (am->ArgMgrDefined("debug")) gdcm::Debug::DebugOn(); int verbose = am->ArgMgrDefined("verbose"); int oververbose = am->ArgMgrDefined("oververbose"); std::string patName = am->ArgMgrGetString("patname", "g^PatientName"); //float zSpacing = am->ArgMgrGetFloat("zSpacing", 1.0); const char *dirIn = am->ArgMgrGetString("dirin"); const char *dirOut = am->ArgMgrGetString("dirout"); bool userDefinedStudy = am->ArgMgrDefined("studyUID"); const char *studyUID = am->ArgMgrGetString("studyUID"); // not described *on purpose* in the Usage ! bool userDefinedSerie = am->ArgMgrDefined("serieUID"); const char *serieUID = am->ArgMgrGetString("serieUID"); int imageDimX = am->ArgMgrGetInt("imdimx",64); int imageDimY = am->ArgMgrGetInt("imdimy",64); int imagePixelSize = am->ArgMgrGetInt("pixelsize", 2); int imagetteLineNumber = am->ArgMgrGetInt("imgline",6); int imagetteRowNumber = am->ArgMgrGetInt("imgcol",6); int nbOfImagesInVolume = am->ArgMgrGetInt("imagesinvolume", imagetteLineNumber*imagetteRowNumber); 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; } /* if unused Param we give up */ if ( am->ArgMgrPrintUnusedLabels() ) { am->ArgMgrUsage(usage); delete am; return 0; } delete am; // ------ we don't need Arguments Manager any longer ------ // ====== Deal with a (single level, single Patient) Directory ====== //std::cout << "dirIn [" << dirIn << "]" << std::endl; if ( ! gdcm::DirList::IsDirectory(dirIn) ) { std::cout << "KO : [" << dirIn << "] is not a Directory." << std::endl; return 0; } else { if (verbose) std::cout << "OK : [" << dirIn << "] is a Directory." << std::endl; } std::string systemCommand; std::string strDirNameout(dirOut); // to please gcc 4 if (verbose) std::cout << "Check for output directory :[" << dirOut << "]." <SetLoadMode(loadMode); f->SetFileName( it->c_str() ); if (verbose) std::cout << "file [" << it->c_str() << "], as imageNumber : " << imageNumber << std::endl; if ( !f->Load() ) { if (verbose) std::cout << "fail to load [" << it->c_str() << "]" << std::endl; f->Delete(); continue; } // Load the pixels in RAM. fh = gdcm::FileHelper::New(f); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!? tabImageData[imageNumber] = (int16_t *)fh->GetImageDataRaw(); if (!tabImageData[imageNumber]) { std::cout << "fail to read [" << it->c_str() << std::endl; continue; } int16_t mini=32000; int16_t maxi=-32000; if (imageNumber == nbOfImagesInVolume-1) { for(imageNumber=0; imageNumber < nbOfImagesInVolume; imageNumber++) { int debMove = (imageNumber%imagetteRowNumber) * imageDimX + (imageNumber/imagetteRowNumber) *imageDimX*imageDimY*imagetteRowNumber; if (verbose) std::cout << "imageNumber " << imageNumber << " debMove " << debMove << std::endl; for(int i=0; i maxi) maxi=*(tabImageData[imageNumber] + i*imageDimY + j); } } } // if (oververbose) // std::cout << " mini = " << mini << " maxi = " << maxi << std::endl; // just to check (actually, it's useless) /* int16_t mini=32000; int16_t maxi=-32000; for (int k=0; k < totalNumberOfPixels; k++) { if (imageTable[k] < mini) mini=imageTable[k]; else if (imageTable[k] > maxi) maxi=imageTable[k]; } // if (oververbose) // std::cout << " mini = " << mini << " maxi = " << maxi << std::endl; /// \todo : FIXME what do I do ? Smallest/Largest Image Pixel Value is vr=US, Pixels are signed ?!? str.str(""); str << mini; fh->InsertEntryString(str.str(),0x0028,0x0106, "US"); // Smallest Image Pixel Value str.str(""); str << maxi; fh->InsertEntryString(str.str(),0x0028,0x0107, "US"); // Largest Image Pixel Value */ imageNumber = 0; // write the imagette // Set the image size str.str(""); str << imageDimX*imagetteRowNumber; fh->InsertEntryString(str.str(),0x0028,0x0011, "US"); // Columns str.str(""); str << imageDimY*imagetteLineNumber; fh->InsertEntryString(str.str(),0x0028,0x0010, "US"); // Rows fh->InsertEntryString(strStudyUID,0x0020,0x000d,"UI"); fh->InsertEntryString(strSerieUID,0x0020,0x000e,"UI"); fh->InsertEntryString(patName,0x0010,0x0010, "PN"); // Patient's Name fh->SetImageData((uint8_t *)imageTable, totalNumberOfPixels * imagePixelSize); // ================================================================================================== // This is a dirty heuristics, but no other way :-( // if Image Orientation (Patient) is not present // I create one, (as Axial) // if Image Position (Patient) is not present // I create one, incrementing zPositionComponent up by user supplied zSpacing // if Slice Location is not present // I create one, as zPositionComponent // // Aware use is free to supply his own one ! /* if (! f->CheckIfEntryExist(0x0020,0x0037) ) // 0020 0037 DS 6 Image Orientation (Patient) { fh->InsertEntryString("1.0\\0.0\\0.0\\0.0\\1.0\\0.0",0x0020,0x0037, "DS"); //[1\0\0\0\1\0] : Axial char charImagePosition[256]; sprintf(charImagePosition,"%f\\0.0\\0.0",zPositionComponent); zPositionComponent += zSpacing; if (! f->CheckIfEntryExist(0x0020,0x0032) ) //0020 0032 DS 3 Image Position (Patient) fh->InsertEntryString(charImagePosition,0x0020,0x0032, "DS"); if (! f->CheckIfEntryExist(0x0020,0x1041) ) // 0020 0x1041 DS 1 Slice Location { sprintf(charImagePosition,"%f",zPositionComponent); fh->InsertEntryString(charImagePosition,0x0020,0x1041, "DS"); } } */ // ================================================================================================== fh->SetWriteTypeToDcmExplVR(); fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE); lastFilename = gdcm::Util::GetName( fullFilename ); std::string fullWriteFilename = strDirNameout + gdcm::GDCM_FILESEPARATOR + lastFilename; if (verbose) std::cout << "Write : [" << fullWriteFilename << "]" << std::endl; if (!fh->Write(fullWriteFilename)) { std::cout << "Fail to write :[" << fullWriteFilename << "]" << std::endl; } //break; } // end : 'write the imagette' else { imageNumber++; } // FIXME : delete just in time! // fh->Delete(); // f->Delete(); } }