X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Example%2FSplitIntoXCoherentDirectories.cxx;h=e8c45cd1517b7f5655de20c64c01de6231b6f6c2;hb=d0f6827609a499057f4bad725522060590af3d82;hp=4fc1d51557ab2464d1c085fb63f4574bc9a64646;hpb=3119a4472f93a8dbb094a9154c214d511dcbd49f;p=gdcm.git diff --git a/Example/SplitIntoXCoherentDirectories.cxx b/Example/SplitIntoXCoherentDirectories.cxx index 4fc1d515..e8c45cd1 100755 --- a/Example/SplitIntoXCoherentDirectories.cxx +++ b/Example/SplitIntoXCoherentDirectories.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: SplitIntoXCoherentDirectories.cxx,v $ Language: C++ - Date: $Date: 2007/10/19 11:53:42 $ - Version: $Revision: 1.2 $ + Date: $Date: 2011/04/20 14:06:50 $ + Version: $Revision: 1.6 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -30,18 +30,18 @@ int main(int argc, char *argv[]) START_USAGE(usage) "\n exXCoherentFileSet :\n ", "Shows the various 'XCoherent' Filesets within a directory ", - "Optionaly copis the images in a Directories tree ", + "Optionaly copies the images in a Directories tree ", "usage: exXCoherentFileSet {dirin=inputDirectoryName} ", " dirout=outputDirectoryName ", " { tag=group-elem | pos | ori } [sort] ", - " [{ write | copy }] [studyUID = ] ", + " [{ write | copy }] [studyUID = ] ", " [ { [noshadowseq] | [noshadow][noseq] } ] [debug] ", " ", " dirin : user wants to analyze *all* the files ", " within the directory ", " copy : user wants to copy the files into a directories tree ", " write : user wants to rewrite the files into a directories tree ", - " each directory with the same 'Series Instance UID' ", + " each directory with the same 'Series Instance UID' ", " dirout : will be created if doesn't exist ", " pos : user wants to split each Single SerieUID Fileset on the ", " 'Image Position ' ", @@ -50,7 +50,7 @@ int main(int argc, char *argv[]) " tag : group-elem (in hexa, no space) ", " the user wants to split on ", " sort : user wants FileHelper to sort the images ", - " Warning : will probabely crah if sort has no meaning ", + " Warning : will probabely crash if sort has no meaning ", " (not only look at image names) ", " studyUID : *aware* user wants to add the serie ", " to an already existing study ", @@ -74,7 +74,7 @@ int main(int argc, char *argv[]) int loadMode; int maxSize; - + const char *dirName = am->ArgMgrGetString("dirin"); if (dirName == 0) { @@ -93,16 +93,16 @@ int main(int argc, char *argv[]) bool ori = ( 0 != am->ArgMgrDefined("ori") ); bool sort = ( 0 != am->ArgMgrDefined("sort") ); bool copy = ( 0 != am->ArgMgrDefined("copy") ); - bool write = ( 0 != am->ArgMgrDefined("write") ); + bool write = ( 0 != am->ArgMgrDefined("write") ); bool verbose = ( 0 != am->ArgMgrDefined("verbose") ); bool tag = ( 0 != am->ArgMgrDefined("tag") ); - + if( copy && write ) { std::cout << "COPY and WRITE are mutually exclusive" << std::endl; delete am; - return 0; - } + return 0; + } if( (tag && (pos || ori)) || (pos && (tag || ori)) || (ori && (tag || pos)) ) { @@ -144,16 +144,17 @@ int main(int argc, char *argv[]) delete am; // ------ we don't need Arguments Manager any longer ------ - GDCM_NAME_SPACE::SerieHelper *s; s = GDCM_NAME_SPACE::SerieHelper::New(); - - GDCM_NAME_SPACE::File *f; + + s->SetLoadMode(GDCM_NAME_SPACE::LD_ALL); // Load everything for each File + s->SetDirectory(dirName, true); // true : recursive exploration GDCM_NAME_SPACE::DirList dirlist(dirName, true); // recursive exploration GDCM_NAME_SPACE::DirListType fileNames = dirlist.GetFilenames(); - GDCM_NAME_SPACE::FileList *l = new GDCM_NAME_SPACE::FileList; + + GDCM_NAME_SPACE::File *f; // Loop on all the gdcm-readable files for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin(); it != fileNames.end(); @@ -161,33 +162,33 @@ int main(int argc, char *argv[]) { if (verbose) std::cout << *it << std::endl; - + if (write) { loadMode = GDCM_NAME_SPACE::LD_ALL; // load any DataElement - maxSize = 0x7fff; // load any length + maxSize = 0x7fff; // load any length } else { loadMode = GDCM_NAME_SPACE::LD_NOSEQ | GDCM_NAME_SPACE::LD_NOSHADOW ; - maxSize = 0x0100; + maxSize = 0x0100; } f = GDCM_NAME_SPACE::File::New(); f->SetLoadMode(loadMode); - f->SetMaxSizeLoadEntry(maxSize); + f->SetMaxSizeLoadEntry(maxSize); f->SetFileName( *it ); f->Load(); - l->push_back(f); + l->push_back(f); } std::string systemCommand; std::string filenameout; - if (write || copy) { + if (write || copy) { if (verbose) std::cout << "Check for output directory :[" << dirNameout << "]." < End of checking supposed-to-be-directory names int nbFiles; @@ -218,19 +219,25 @@ int main(int argc, char *argv[]) // For all the Single SerieUID Files Sets of the GDCM_NAME_SPACE::Serie - //GDCM_NAME_SPACE::FileList *l = s->GetFirstSingleSerieUIDFileSet();//===> Ignore 'Serie UID" + // GDCM_NAME_SPACE::FileList *l = s->GetFirstSingleSerieUIDFileSet(); + + l = s->GetFirstSingleSerieUIDFileSet(); + if (l == NULL) { + std::cout << "No Serie found ?!?" << std::endl; + exit (0); + } GDCM_NAME_SPACE::XCoherentFileSetmap xcm; std::string serieUID; std::string currentSerieWriteDir = ""; std::string xCoherentWriteDir = ""; - std::string xCoherentName = ""; + std::string xCoherentName = ""; std::string serieDirectory; std::string lastFilename; std::string rep("_"); int controlCount = 0; - + // 'Study Instance UID' // The user is allowed to create his own Study, // keeping the same 'Study Instance UID' for various images @@ -244,16 +251,19 @@ int main(int argc, char *argv[]) strStudyUID = studyUID; } -// while (l) // for each 'Single SerieUID FileSet' //===> Ignore 'Serie UID" -// { + while (l) // for each 'Single SerieUID FileSet' //===> Ignore 'Serie UID" + { + currentSerieWriteDir = ""; nbFiles = l->size() ; if ( l->size() > 2 ) // ignore a Directory with less than 2 images. // Why not ? Just an example, for testing! { // Just not to make too many modif in the code - serieUID = "SingleSerie"; //s->GetCurrentSerieUIDFileSetUID(); + //serieUID = "SingleSerie"; // s->GetCurrentSerieUIDFileSetUID(); + serieUID = s->GetCurrentSerieUIDFileSetUID(); + GDCM_NAME_SPACE::Util::ReplaceSpecChar(serieUID, rep); - + // --- for write if (write || copy) { @@ -267,7 +277,7 @@ int main(int argc, char *argv[]) std::cout << "[" << currentSerieWriteDir<< "]" << std::endl; // if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(currentSerieWriteDir) ) { - systemCommand = "mkdir " + currentSerieWriteDir; + systemCommand = "mkdir \"" + currentSerieWriteDir + "\""; system( systemCommand.c_str()); if (verbose) std::cout << "1 " <SplitOnOrientation(l); else if (pos) xcm = s->SplitOnPosition(l); else if (groupelem != 0) { - - std:: cout << GDCM_NAME_SPACE::Global::GetDicts()->GetDefaultPubDict()->GetEntry(groupelem[0],groupelem[1])->GetName() << std::endl; + // Crashes if DataElement not found + //std:: cout << GDCM_NAME_SPACE::Global::GetDicts()->GetDefaultPubDict()->GetEntry(groupelem[0],groupelem[1])->GetName() << std::endl; xcm = s->SplitOnTagValue(l, groupelem[0],groupelem[1] ); } - + GDCM_NAME_SPACE::FileHelper *fh; - + for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin(); i != xcm.end(); ++i) { xCoherentName = (*i).first; if (verbose) - std::cout << "xCoherentName = " << xCoherentName << std::endl; + std::cout << "==========================================xCoherentName = " << xCoherentName << std::endl; GDCM_NAME_SPACE::Util::ReplaceSpecChar(xCoherentName, rep); // --- for write if (write || copy) @@ -310,7 +317,7 @@ GDCM_NAME_SPACE::Debug::DebugOn(); xCoherentWriteDir = currentSerieWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR+ xCoherentName; // if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(xCoherentWriteDir) ) { - systemCommand = "mkdir " + xCoherentWriteDir; + systemCommand = "mkdir \"" + xCoherentWriteDir + "\""; system( systemCommand.c_str()); if (verbose) std::cout << "2 " << systemCommand << std::endl; @@ -334,12 +341,12 @@ GDCM_NAME_SPACE::Debug::DebugOn(); // OrderFileList() causes trouble, since some files // (eg:MIP views) don't have 'Position', now considered as mandatory // --> Activated on user demand. - - if (sort) { + + if (sort) { s->OrderFileList((*i).second); // sort the XCoherent Fileset std::cout << "ZSpacing for the file set " << s->GetZSpacing() << std::endl; - } + } std::string strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); @@ -349,20 +356,18 @@ GDCM_NAME_SPACE::Debug::DebugOn(); { controlCount ++; fileName = (*it2)->GetFileName(); - std::cout << " " << fileName << std::endl; - // --- for write lastFilename = GDCM_NAME_SPACE::Util::GetName( fileName ); - filenameout = xCoherentWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR+ lastFilename; + filenameout = xCoherentWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR+ lastFilename; if (write) { - fh = GDCM_NAME_SPACE::FileHelper::New( (*it2) ); + fh = GDCM_NAME_SPACE::FileHelper::New( (*it2) ); fh->SetKeepOverlays( true ); fh->InsertEntryString(strSerieUID,0x0020,0x000e,"UI"); unsigned int dataSize = fh->GetImageDataRawSize(); uint8_t *imageData = fh->GetImageDataRaw();// somewhat important : Loads the Pixels in memory ! if (!imageData) - std::cout << "fail to read [" << (*it2)->GetFileName() << std::endl; + std::cout << "fail to read [" << (*it2)->GetFileName() << std::endl; fh->SetWriteTypeToDcmExplVR(); fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE); if (!fh->Write(filenameout)) @@ -371,24 +376,24 @@ GDCM_NAME_SPACE::Debug::DebugOn(); << std::endl; } fh->Delete(); - } + } else if (copy) { - systemCommand = "cp " + fileName + " " + filenameout; + systemCommand = "cp \"" + fileName + "\" " + filenameout + "\""; system( systemCommand.c_str()); - } + } if (verbose) std::cout << "3 " << systemCommand << std::endl; - } - - std::cout << std::endl; + } } + std::cout << std::endl; } - // l = s->GetNextSingleSerieUIDFileSet(); //===> Ignore 'Serie UID" + l = s->GetNextSingleSerieUIDFileSet(); + } if ( controlCount == 0 ) std::cout << "No suitable file was found!" << std::endl; - + s->Delete(); return 0; }