--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: ToMRIregister.cxx,v $
+ Language: C++
+ Date: $Date: 2006/07/26 17:15:27 $
+ 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 "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmDebug.h"
+#include "gdcmDirList.h"
+#include "gdcmUtil.h"
+#include "gdcmArgMgr.h"
+#include <iostream>
+#include <sstream>
+
+bool AquisitionTime_0008_0032_Compare(gdcm::File *file1, gdcm::File *file2);
+
+bool AquisitionTime_0008_0032_Compare(gdcm::File *file1, gdcm::File *file2)
+{
+ return file1->GetEntryString(0x0008,0x0032) < file2->GetEntryString(0x0008,0x0032);
+}
+
+int main(int argc, char *argv[])
+{
+
+ START_USAGE(usage)
+ "\n ToMriregister :\n ",
+ " - Converts the Siemens Sonata MRI '*tfl2d1' ",
+ " to be processable by MriRegister software ",
+ " - May be used as a template for gdcm::SerieHelper use. ",
+ " ",
+ "usage: ToMriRegister dirin=inputDirectoryName ",
+ " dirout=outputDirectoryName ",
+ " [ { [noshadowseq] | [noshadow][noseq] } ] [debug] ",
+ " ",
+ " inputDirectoryName : user wants to analyze *all* the files ",
+ " within the directory ",
+ " 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 : developer 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 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;
+ }
+
+ const char *dirIn = am->ArgMgrGetString("dirin");
+ if (dirIn == 0)
+ {
+ std::cout <<std::endl
+ << "'dirin=' must be present;"
+ << std::endl;
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
+ }
+
+ const char *dirOut = am->ArgMgrGetString("dirout");
+ if (dirOut == 0)
+ {
+ std::cout <<std::endl
+ << "'dirout=' must be present;"
+ << std::endl;
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
+ }
+
+ /* 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 ------
+
+ // ======================== more checking on the params ==============
+
+ 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 << "]."
+ <<std::endl;
+ if ( ! gdcm::DirList::IsDirectory(dirOut) ) // dirout not found
+ {
+ systemCommand = "mkdir " + strDirNameout; // create it!
+ if (verbose)
+ std::cout << systemCommand << std::endl;
+ system (systemCommand.c_str());
+ if ( ! gdcm::DirList::IsDirectory(dirOut) ) // be sure it worked
+ {
+ std::cout << "KO : not a dir : [" << dirOut
+ << "] (creation failure ?)" << std::endl;
+ return 0;
+
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "Directory [" << dirOut << "] created." << std::endl;
+ }
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "Output Directory [" << dirOut
+ << "] already exists; Used as is." << std::endl;
+ }
+
+ // ========================== Now, we can do the job! ================
+
+ // Just to see *all* the file names:
+
+ gdcm::DirList dirList(dirIn,true); // gets (recursively) the file list
+ gdcm::DirListType fileList = dirList.GetFilenames();
+ for( gdcm::DirListType::iterator it = fileList.begin();
+ it != fileList.end();
+ ++it )
+ {
+ std::cout << "file [" << it->c_str() << "]" << std::endl;
+ }
+
+ gdcm::SerieHelper *s;
+
+ s = gdcm::SerieHelper::New();
+ s->SetLoadMode(gdcm::LD_NOSEQ); // Don't load Sequences
+
+ // we could choose to ignore some Files
+ //gdcm::TagKey t(0x0010,0x0024); // [Sequence Name]
+ // Keep only files where restriction is true
+ //s->AddRestriction(t, "*tfl2d1 ", gdcm::GDCM_EQUAL);
+
+ s->SetDirectory(dirIn, true); // true : recursive exploration
+
+/*
+ std::cout << " ---------------------------------------- "
+ << "'Single UID' Filesets found in :["
+ << dirName << "]" << std::endl;
+
+ s->Print();
+ std::cout << " ------------------------------------- Result after splitting"
+ << std::endl;
+*/
+ int nbFiles;
+ std::string fullFilename, lastFilename;
+ char fullWriteFilename[1024]; // should be enough.
+
+ std::ostringstream str;
+
+ gdcm::XCoherentFileSetmap xcm;
+ gdcm::FileHelper *fh;
+
+ // will be used for ordering.
+ s->SetUserLessThanFunction(AquisitionTime_0008_0032_Compare);
+ int serieNumber = 0;
+ int sliceNumber = 0;
+ int imageNumber = 0;
+
+ // For all the Single SerieUID Files Sets of the gdcm::Serie
+ gdcm::FileList *l = s->GetFirstSingleSerieUIDFileSet();
+ while (l)
+ {
+ nbFiles = l->size() ;
+ if ( l->size() < 8 ) // Hope we skip Scout views !
+ {
+ std::cout << "Ignore the 'Single SerieUID' FileSet :["
+ << s->GetCurrentSerieUIDFileSetUID()
+ << "] " << nbFiles << " long" << std::endl;
+ std::cout << "-----------------------------------" << std::endl;
+ }
+ else
+ {
+ std::cout << "Split the 'Single SerieUID' FileSet :["
+ << s->GetCurrentSerieUIDFileSetUID()
+ << "] " << nbFiles << " long" << std::endl;
+ std::cout << "-----------------------------------" << std::endl;
+
+ xcm = s->SplitOnPosition(l);
+
+ //int sliceNumber = 0;
+
+ for (gdcm::XCoherentFileSetmap::iterator i = xcm.begin();
+ i != xcm.end();
+ ++i)
+ {
+ std::cout << "Position : ";
+ std::cout << "[" << (*i).first << "]" << std::endl;
+
+ s->OrderFileList((*i).second); // sort the current XCoherent Fileset
+
+ //int imageNumber = 0;
+ for ( gdcm::FileList::iterator it = ((*i).second)->begin();
+ it != ((*i).second)->end();
+ ++it)
+ {
+
+ // Set the DataElements MriRegister needs to be happy
+ // Probabely one of the following (check it !):
+ /*
+ 0020 0011 IS 1 Series Number
+ 0020 0012 IS 1 Acquisition Number
+ 0020 0013 IS 1 Instance Number
+ */
+
+ str.str("");
+ str << serieNumber;
+ (*it)->InsertEntryString(str.str(),0x0020,0x0011, "IS"); // Series Number
+
+ str.str("");
+ str << imageNumber;
+ (*it)->InsertEntryString(str.str(),0x0020,0x0013, "IS"); // Instance Number
+
+ // Load the pixels in RAM.
+
+ fh = gdcm::FileHelper::New(*it);
+ uint8_t *imageData = fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
+ if (!imageData)
+ std::cout << "fail to read [" << (*it)->GetFileName() << std::endl;
+ fh->SetWriteTypeToDcmExplVR();
+ fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE);
+
+ // forge the file name
+
+ fullFilename = (*it)->GetFileName();
+ lastFilename = gdcm::Util::GetName( fullFilename );
+ //fullWriteFilename = strDirNameout + gdcm::GDCM_FILESEPARATOR
+ // + lastFilename;
+ sprintf(fullWriteFilename, "%s%c%04d-%04d-%04d.dcm",
+ dirOut, gdcm::GDCM_FILESEPARATOR,
+ serieNumber, sliceNumber, imageNumber);
+ if (verbose)
+ std::cout << fullFilename << " -> " << fullWriteFilename << std::endl;
+
+ // Write it, now
+
+ if (!fh->Write(fullWriteFilename))
+ {
+ std::cout << "Fail to write :[" << fullWriteFilename << "]"
+ << std::endl;
+ }
+
+ ///\todo FIXME segfaults if uncommented ?!?
+ // delete(imageData);
+ (*it)->Delete();
+ fh->Delete();
+
+ imageNumber++;
+
+ }
+ std::cout << std::endl;
+ sliceNumber++;
+ }
+ }
+ serieNumber++;
+ l = s->GetNextSingleSerieUIDFileSet();
+ }
+ s->Delete();
+ return 0;
+}
projects / gdcm.git / commitdiff