--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: AnonymizeMultiPatient.cxx,v $
+ Language: C++
+ Date: $Date: 2006/05/30 08:26:36 $
+ 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 "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmCommon.h"
+#include "gdcmUtil.h"
+#include "gdcmDebug.h"
+#include "gdcmDirList.h"
+
+#include "gdcmDicomDir.h"
+#include "gdcmDicomDirPatient.h"
+#include "gdcmDicomDirStudy.h"
+#include "gdcmDicomDirSerie.h"
+#include "gdcmDicomDirImage.h"
+
+#include "gdcmArgMgr.h"
+
+#include <iostream>
+
+
+int main(int argc, char *argv[])
+{
+ START_USAGE(usage)
+ " \n AnonymizeMultiPatient :\n ",
+ " AnonymizeMultiPatient a full gdcm-readable Dicom image ",
+ " Warning : the image is OVERWRITTEN ",
+ " to preserve image integrity, use a copy. ",
+ " usage: AnonymizeMultiPatient dirin=inputDirectoryName dirout=outputDirectoryName",
+ " listOfElementsToRubOut : group-elem,g2-e2,... (in hexa, no space) ",
+ " of extra Elements to rub out ",
+ " 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 : user wants to run the program in 'debug mode' ",
+ 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 0;
+ }
+ const char *dirName = am->ArgMgrGetString("dirin");
+ if ( dirName == NULL )
+ {
+ delete am;
+ return 0;
+ }
+
+ /*
+ char *outputDirName = am->ArgMgrWantString("dirout",usage);
+ if ( outputDirName == NULL )
+ {
+ delete am;
+ return 0;
+ }
+ */
+
+ bool verbose = am->ArgMgrDefined("verbose");
+
+ if (am->ArgMgrDefined("debug"))
+ gdcm::Debug::DebugOn();
+
+ 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 rubOutNb;
+ uint16_t *elemsToRubOut = am->ArgMgrGetXInt16Enum("rubout", &rubOutNb);
+
+ // if unused Param we give up
+ if ( am->ArgMgrPrintUnusedLabels() )
+ {
+ am->ArgMgrUsage(usage);
+ delete am;
+ return 0;
+ }
+
+ delete am; // we don't need Argument Manager any longer
+
+ // ----------------------------------------------------------
+
+ // ----- Begin Processing -----
+
+ gdcm::DicomDir *dcmdir;
+
+ // we ask for Directory parsing
+
+ dcmdir = gdcm::DicomDir::New( );
+
+ dcmdir->SetLoadMode(loadMode);
+ dcmdir->SetDirectoryName(dirName);
+ dcmdir->Load();
+
+
+
+ gdcm::DicomDirPatient *pa;
+ gdcm::DicomDirStudy *st;
+ gdcm::DicomDirSerie *se;
+ gdcm::DicomDirVisit *vs;
+ gdcm::DicomDirImage *im;
+
+ // Test if the DicomDir contains any Patient
+ pa = dcmdir->GetFirstPatient();
+ if ( pa == 0)
+ {
+ std::cout<<" DicomDir '"<< dirName
+ <<" has no patient"<<std::endl
+ <<" ...Failed"<<std::endl;
+
+ dcmdir->Delete();
+ return 1;
+ }
+
+ if ( verbose )
+ std::cout << "-------------------------- Directory [" << dirName << "] parsed" << std::endl;
+
+// Since files may be help in a Directory tree-like structure
+// we should have to duplicate this structure.
+// No time to code that stuff
+// --> We 'AnonymizeNoLoad' (overwrite the files)
+
+// Do not remove the commented out lines.
+// They will be usefull in a further program.
+/*
+ std::string systemCommand;
+
+ std::cout << "Check for output directory :[" << outputDirName << "]."
+ <<std::endl;
+ if ( ! gdcm::DirList::IsDirectory(outputDirName) ) // dirout not found
+ {
+ std::string strDirNameout(outputDirName); // to please gcc 4
+ systemCommand = "mkdir " +strDirNameout; // create it!
+ if (verbose)
+ std::cout << systemCommand << std::endl;
+ system (systemCommand.c_str());
+ if ( ! gdcm::DirList::IsDirectory(outputDirName) ) // be sure it worked
+ {
+ std::cout << "KO : not a dir : [" << outputDirName << "] (creation failure ?)" << std::endl;
+ exit(0);
+ }
+ else
+ {
+ std::cout << "Directory [" << outputDirName << "] created." << std::endl;
+ }
+ }
+ else
+ {
+ std::cout << "Output Directory [" << outputDirName << "] already exists; Used as is." << std::endl;
+ }
+*/
+
+ gdcm::File *f;
+ gdcm::FileHelper *fh;
+ // std::string outputFileName;
+
+ std::string codedName;
+ while (pa)
+ {
+ if (verbose)
+ {
+ std::cout << "Pat.Name:[" << pa->GetEntryString(0x0010, 0x0010) <<"]"; // Patient's Name
+ std::cout << " Pat.ID:[";
+ std::cout << pa->GetEntryString(0x0010, 0x0020) << "]" << std::endl; // Patient ID
+ }
+ std::string patName = pa->GetEntryString(0x0010, 0x0010);
+ //codedName = "g^" + gdcm::Util::ConvertToMD5(patName); // just to be sure MD5 is not guilty
+ std::string fullFileName;
+ if (verbose)
+ std::cout << patName << " --> " << codedName << std::endl;
+
+ st = pa->GetFirstStudy();
+ while ( st )
+ { // on degouline les STUDY de ce patient
+ if (verbose)
+ {
+ std::cout << "--- Stud.descr:[" << st->GetEntryString(0x0008, 0x1030) << "]"; // Study Description
+ std::cout << " Stud.ID:[" << st->GetEntryString(0x0020, 0x0010) << "]"; // Study ID
+ std::cout << std::endl;
+ }
+ se = st->GetFirstSerie();
+ while ( se )
+ { // on degouline les SERIES de cette study
+ if (verbose)
+ {
+ std::cout << "--- --- Ser.Descr:["<< se->GetEntryString(0x0008, 0x103e) << "]"; // Series Description
+ std::cout << " Ser.nb:[" << se->GetEntryString(0x0020, 0x0011) << "]"; // Series number
+ std::cout << " Mod.:[" << se->GetEntryString(0x0008, 0x0060) << "]"; // Modality
+ std::cout << " Serie Inst.UID.:[" << se->GetEntryString(0x0020, 0x000e) << "]"; // Series Instance UID
+ std::cout << std::endl;
+ }
+
+ im = se->GetFirstImage();
+ std::string ReferencedFileID;
+ while ( im )
+ { // on degouline les IMAGEs de cette serie
+ ReferencedFileID = im->GetEntryString(0x0004, 0x1500);
+ if (verbose)
+ {
+ std::cout << "--- --- --- "<< " IMAGE Ref. File ID :[" << ReferencedFileID
+ << "]" << std::endl; // File name (Referenced File ID)
+ }
+ f = gdcm::File::New( );
+ f->SetLoadMode(loadMode);
+ fullFileName = dirName;
+
+ std::cout << "fullFileName (1) " << fullFileName << std::endl;
+ std::cout << "ReferencedFileID " << ReferencedFileID << std::endl;
+ fullFileName = fullFileName + "/" + ReferencedFileID;
+ std::cout << "fullFileName (2) " << fullFileName << std::endl;
+
+ f->SetFileName( fullFileName );
+
+ if ( !f->Load() )
+ std::cout << "Load failed for [" << fullFileName << "]" << std::endl;
+ else
+ std::cout << "Load successed for [" << fullFileName << "]" << std::endl;
+
+ //
+ // Choose the fields to anonymize.
+ //
+
+ // Institution name
+ f->AddAnonymizeElement( 0x0008, 0x0080, "Xanadoo" );
+
+ // Patient's name
+ f->AddAnonymizeElement( 0x0010, 0x0010, codedName );
+
+ // Patient's ID
+ f->AddAnonymizeElement( 0x0010, 0x0020,"1515" );
+ // Patient's Birthdate
+ f->AddAnonymizeElement( 0x0010, 0x0030,"11111111" );
+ // Patient's Adress
+ f->AddAnonymizeElement( 0x0010, 0x1040,"Sing-sing" );
+ // Patient's Mother's Birth Name
+ f->AddAnonymizeElement( 0x0010, 0x1060,"g^Vampirella" );
+
+ // Study Instance UID
+ // we may not brutaly overwrite it
+ //f->AddAnonymizeElement( 0x0020, 0x000d, "9.99.999.9999" );
+
+ // Telephone
+ f->AddAnonymizeElement(0x0010, 0x2154, "3615" );
+
+ // deal with user defined Elements set
+
+std::cout << "rubOutNb " << rubOutNb << std::endl;
+ for (int ri=0; ri<rubOutNb; ri++)
+ {
+ f->AddAnonymizeElement((uint32_t)elemsToRubOut[2*ri],
+ (uint32_t)elemsToRubOut[2*ri+1],"*" );
+ }
+
+ // The gdcm::File is modified in memory
+ // f->AnonymizeFile();
+
+ //
+ // Overwrite the file
+ //
+ // The gdcm::File remains untouched in memory
+ f->AnonymizeNoLoad();
+
+ // ============================================================
+ // Write a new file
+ // ============================================================
+
+ //
+ // No need to load the pixels in memory.
+ // File will be overwritten
+
+ // Do not remove the commented out lines.
+ // They will be usefull in a further program.
+ //
+/*
+ // Get the Pixels
+ fh = gdcm::FileHelper::New(f);
+
+ // unit8_t DOESN'T mean it's mandatory for the image to be a 8 bits one !
+ // Feel free to cast if you know it's not.
+
+ uint8_t *imageData = fh->GetImageData();
+
+ if ( imageData == 0 )
+ {
+ std::cerr << "Sorry, Pixels of" << im->GetEntryString(0x0004, 0x1500) <<" are not "
+ << " gdcm-readable." << std::endl
+ << "Use AnonymizeNoLoad" << std::endl;
+ f->Delete();
+ fh->Delete();
+ break;
+ }
+
+ // Since we just Anonymized the file, we *know* no modification
+ // was performed on the pixels.
+ // The written image will not appear as a 'Secondary Captured image'
+ // nor as a DERIVED one
+
+ fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE);
+ outputFileName = outputDirName + "/" + im->GetEntryString(0x0004, 0x1500);
+ fh->WriteDcmExplVR(outputFileName);
+ std::cout <<"End Anonymize" << std::cout;
+
+ fh->Delete();
+*/
+
+ f->Delete();
+ f->ClearAnonymizeList();
+
+ im = se->GetNextImage();
+ }
+ se = st->GetNextSerie();
+ }
+ st = pa->GetNextStudy();
+ }
+
+ pa = dcmdir->GetNextPatient();
+ }
+
+}
+
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