--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: SplitIntoXCoherentDirectories.cxx,v $
+ Language: C++
+ Date: $Date: 2007/10/01 09:40:32 $
+ Version: $Revision: 1.1 $
+
+ 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 "gdcmSerieHelper.h"
+#include "gdcmFileHelper.h"
+#include "gdcmFile.h"
+#include "gdcmDebug.h"
+#include <iostream>
+#include "gdcmDirList.h"
+#include "gdcmUtil.h"
+#include "gdcmArgMgr.h"
+#include "gdcmDictSet.h" // for GetName
+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 ",
+ "usage: exXCoherentFileSet {dirin=inputDirectoryName} ",
+ " dirout=outputDirectoryName ",
+ " { tag=group-elem | pos | ori } [sort] ",
+ " [{ 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' ",
+ " dirout : will be created if doesn't exist ",
+ " pos : user wants to split each Single SerieUID Fileset on the ",
+ " 'Image Position ' ",
+ " ori : user wants to split each Single SerieUID Fileset on the ",
+ " 'Image Orientation ' ",
+ " 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 ",
+ " (not only look at image names) ",
+ " studyUID : *aware* user wants to add the serie ",
+ " to an already existing study ",
+ " 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_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
+
+ if (am->ArgMgrDefined("usage") || argc == 1)
+ {
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
+ }
+
+ if (am->ArgMgrDefined("debug"))
+ GDCM_NAME_SPACE::Debug::DebugOn();
+
+ int loadMode;
+ int maxSize;
+
+ const char *dirName = am->ArgMgrGetString("dirin");
+ if (dirName == 0)
+ {
+ std::cout <<std::endl
+ << "'dirin=' must be present;"
+ << std::endl;
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
+ }
+
+ const char *dirNameout;
+ dirNameout = am->ArgMgrGetString("dirout",".");
+
+ bool pos = ( 0 != am->ArgMgrDefined("pos") );
+ 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 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;
+ }
+
+ if( (tag && (pos || ori)) || (pos && (tag || ori)) || (ori && (tag || pos)) )
+ {
+ std::cout << " POS, ORI and TAG are mutually exclusive" << std::endl;
+ delete am;
+ return 0;
+ }
+
+ if( (!tag && !pos && !ori))
+ {
+ std::cout << " One of POS, ORI and TAG is mandatory!" << std::endl;
+ delete am;
+ return 0;
+ }
+ int nb;
+ uint16_t *groupelem;
+ if (tag)
+ {
+ groupelem = am->ArgMgrGetXInt16Enum("tag", &nb);
+ if (nb != 1)
+ {
+ std::cout << "TAG : one and only one group,elem!" << std::endl;
+ delete am;
+ return 0;
+ }
+ }
+
+ bool userDefinedStudy = ( 0 != am->ArgMgrDefined("userDefinedStudy") );
+ const char *studyUID = am->ArgMgrGetString("studyUID");
+
+ /* 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 ------
+
+
+
+ GDCM_NAME_SPACE::SerieHelper *s;
+ s = GDCM_NAME_SPACE::SerieHelper::New();
+
+ GDCM_NAME_SPACE::File *f;
+
+ 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;
+// Loop on all the gdcm-readable files
+ for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin();
+ it != fileNames.end();
+ ++it)
+ {
+ if (verbose)
+ std::cout << *it << std::endl;
+
+ if (write) {
+ loadMode = GDCM_NAME_SPACE::LD_ALL; // load any DataElement
+ maxSize = 0x7fff; // load any length
+ } else {
+ loadMode = GDCM_NAME_SPACE::LD_NOSEQ | GDCM_NAME_SPACE::LD_NOSHADOW ;
+ maxSize = 0x0100;
+ }
+
+ f = GDCM_NAME_SPACE::File::New();
+ f->SetLoadMode(loadMode);
+ f->SetMaxSizeLoadEntry(maxSize);
+ f->SetFileName( *it );
+ f->Load();
+ l->push_back(f);
+ }
+
+ std::string systemCommand;
+ std::string filenameout;
+ if (write || copy) {
+ if (verbose)
+ std::cout << "Check for output directory :[" << dirNameout << "]."
+ <<std::endl;
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNameout) ) // dirout not found
+ {
+ std::string strDirNameout(dirNameout); // to please gcc 4
+ systemCommand = "mkdir " +strDirNameout; // create it!
+ if (verbose)
+ std::cout << systemCommand << std::endl;
+ system (systemCommand.c_str());
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNameout) ) // be sure it worked
+ {
+ std::cout << "KO : not a dir : [" << dirNameout << "] (creation failure ?)"
+ << std::endl;
+ return 0;
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "Directory [" << dirNameout << "] created." << std::endl;
+ }
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "Output Directory [" << dirNameout
+ << "] already exists; Used as is."
+ << std::endl;
+ }
+ }
+
+ // --> End of checking supposed-to-be-directory names
+
+ int nbFiles;
+ std::string fileName;
+
+ // 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::XCoherentFileSetmap xcm;
+
+ std::string serieUID;
+ std::string currentSerieWriteDir = "";
+ std::string xCoherentWriteDir = "";
+ 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
+ // The user may add images to a 'Manufacturer Study',
+ // adding new Series to an already existing Study
+ std::string strStudyUID;
+ if (write) {
+ if ( !userDefinedStudy )
+ strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+ else
+ strStudyUID = studyUID;
+ }
+
+// while (l) // for each 'Single SerieUID FileSet' //===> Ignore 'Serie UID"
+// {
+ 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 = "aaaa"; //s->GetCurrentSerieUIDFileSetUID();
+ GDCM_NAME_SPACE::Util::ReplaceSpecChar(serieUID, rep);
+
+ // --- for write
+ if (write || copy)
+ {
+ currentSerieWriteDir = currentSerieWriteDir + dirNameout;
+ unsigned int l = strlen(dirNameout)-1;
+ if ( dirNameout[l] != '/' && dirNameout[l] != '\\')
+ currentSerieWriteDir = currentSerieWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR;
+
+ currentSerieWriteDir = currentSerieWriteDir + serieUID;
+ if (verbose)
+ std::cout << "[" << currentSerieWriteDir<< "]" << std::endl;
+ // if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(currentSerieWriteDir) )
+ {
+ systemCommand = "mkdir " + currentSerieWriteDir;
+ system( systemCommand.c_str());
+ if (verbose)
+ std::cout << "1 " <<systemCommand << std::endl;
+ }
+ }
+ // --- end for write
+
+ std::cout << "Split the 'Single SerieUID' FileSet :["
+ << serieUID
+ << "] " << nbFiles << " long" << std::endl;
+ std::cout << "-----------------------------------" << std::endl;
+
+ if (ori)
+ xcm = s->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;
+
+ 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;
+ GDCM_NAME_SPACE::Util::ReplaceSpecChar(xCoherentName, rep);
+ // --- for write
+ if (write || copy)
+ {
+ xCoherentWriteDir = currentSerieWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR+ xCoherentName;
+ // if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(xCoherentWriteDir) )
+ {
+ systemCommand = "mkdir " + xCoherentWriteDir;
+ system( systemCommand.c_str());
+ if (verbose)
+ std::cout << "2 " << systemCommand << std::endl;
+ }
+ }
+ // --- end for write
+
+ if (ori)
+ std::cout << "Orientation : ";
+ else if (pos)
+ std::cout << "Position : ";
+ else if (groupelem != 0)
+ std::cout << "Tag (" << std::hex << groupelem[0]
+ << "|" << groupelem[1] << ") value : ";
+ std::cout << "[" << (*i).first << "]" << std::endl;
+
+ if (verbose)
+ std::cout << "xCoherentName [" << xCoherentName << "]" << std::endl;
+
+ // Within a 'just to see' program,
+ // OrderFileList() causes trouble, since some files
+ // (eg:MIP views) don't have 'Position', now considered as mandatory
+ // --> Activated on user demand.
+
+ 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();
+
+ for (GDCM_NAME_SPACE::FileList::iterator it2 = ((*i).second)->begin();
+ it2 != ((*i).second)->end();
+ ++it2)
+ {
+ 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;
+ if (write)
+ {
+ 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;
+ fh->SetWriteTypeToDcmExplVR();
+ fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
+ if (!fh->Write(filenameout))
+ {
+ std::cout << "Fail to write :[" << filenameout << "]"
+ << std::endl;
+ }
+ }
+ else if (copy)
+ {
+ systemCommand = "cp " + fileName + " " + filenameout;
+ system( systemCommand.c_str());
+ }
+ if (verbose)
+ std::cout << "3 " << systemCommand << std::endl;
+ fh->Delete();
+ }
+
+ std::cout << std::endl;
+ }
+ }
+ // l = s->GetNextSingleSerieUIDFileSet(); //===> Ignore 'Serie UID"
+
+ if ( controlCount == 0 )
+ std::cout << "No suitable file was found!" << std::endl;
+
+ s->Delete();
+ return 0;
+}
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff