Program: gdcm
Module: $RCSfile: AnonymizeMultiPatient.cxx,v $
Language: C++
- Date: $Date: 2006/05/30 08:26:36 $
- Version: $Revision: 1.1 $
+ Date: $Date: 2006/05/31 16:16:04 $
+ Version: $Revision: 1.2 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
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 "gdcmDocEntry.h"
#include "gdcmDicomDir.h"
#include "gdcmDicomDirPatient.h"
#include "gdcmDicomDirStudy.h"
+#include "gdcmDicomDirVisit.h"
#include "gdcmDicomDirSerie.h"
#include "gdcmDicomDirImage.h"
+#include "gdcmDirList.h"
+#include "gdcmDebug.h"
+#include "gdcmUtil.h"
+#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
#include "gdcmArgMgr.h"
#include <iostream>
+/**
+ * \brief Explores recursively the given directory
+ * orders the gdcm-readable found Files
+ * according their Patient/Study/Serie/Image characteristics
+ * and anomymizes (NoLoad) them, creates a different name for each Patient.
+ */
-int main(int argc, char *argv[])
+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",
+ " usage: AnonymizeMultiPatient dirin=inputDirectoryName ",
" 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' ",
+ " 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);
delete am;
return 0;
}
- const char *dirName = am->ArgMgrGetString("dirin");
- if ( dirName == NULL )
+ const char * name = am->ArgMgrGetString("dirin");
+ if ( name == NULL )
{
delete am;
return 0;
}
- /*
- char *outputDirName = am->ArgMgrWantString("dirout",usage);
- if ( outputDirName == NULL )
- {
- delete am;
- return 0;
- }
- */
-
+ std::string dirName = name;
+
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
loadMode |= gdcm::LD_NOSEQ;
}
+
int rubOutNb;
uint16_t *elemsToRubOut = am->ArgMgrGetXInt16Enum("rubout", &rubOutNb);
- // if unused Param we give up
+ // ----------- if unused Param we give up
if ( am->ArgMgrPrintUnusedLabels() )
{
am->ArgMgrUsage(usage);
}
delete am; // we don't need Argument Manager any longer
-
+
+
// ----------------------------------------------------------
- // ----- Begin Processing -----
+
+ // ----- Begin Processing -----
gdcm::DicomDir *dcmdir;
// we ask for Directory parsing
dcmdir = gdcm::DicomDir::New( );
-
dcmdir->SetLoadMode(loadMode);
dcmdir->SetDirectoryName(dirName);
dcmdir->Load();
-
+ if ( verbose )
+ std::cout << "======================= End Parsing Directory" << std::endl;
+
+ // ----- Check the result
+
+ if ( !dcmdir->GetFirstPatient() )
+ {
+ std::cout << "No patient found (?!?). Exiting."
+ << std::endl;
+ dcmdir->Delete();
+ return 1;
+ }
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)
+ gdcm::DicomDirImage *im;
-// 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!
+ std::string codedName;
+ std::string fullFileName;
+ std::string patName;
+
+ gdcm::File *f;
+
+ pa = dcmdir->GetFirstPatient();
+ while ( pa )
+ { // on degouline les PATIENT du DICOMDIR
+ patName = pa->GetEntryString(0x0010, 0x0010);
+ codedName = "g^" + gdcm::Util::ConvertToMD5(patName);
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();
+ 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);
+ { // on degouline les Images de cette serie
+ fullFileName = dirName;
+ fullFileName += gdcm::GDCM_FILESEPARATOR;
+ fullFileName += im->GetEntryString(0x0004, 0x1500);
if (verbose)
- {
- std::cout << "--- --- --- "<< " IMAGE Ref. File ID :[" << ReferencedFileID
- << "]" << std::endl; // File name (Referenced File ID)
- }
+ std::cout << "FileName " << fullFileName << std::endl;
+
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;
+ std::cout << "Load failed for [" << fullFileName << "]" << std::endl;
else
- std::cout << "Load successed for [" << fullFileName << "]" << std::endl;
-
+ if (verbose)
+ std::cout << "Load successed for [" << fullFileName << "]" << std::endl;
+
//
// Choose the fields to anonymize.
//
// 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],"*" );
+ (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();
-*/
+ //
+ // Overwrite the file
+ //
+ // The gdcm::File remains untouched in memory
+
+ f->AnonymizeNoLoad();
- f->Delete();
- f->ClearAnonymizeList();
-
- im = se->GetNextImage();
- }
- se = st->GetNextSerie();
- }
- st = pa->GetNextStudy();
- }
-
+ f->ClearAnonymizeList();
+ f->Delete();
+
+ im = se->GetNextImage();
+ }
+ se = st->GetNextSerie();
+ }
+ st = pa->GetNextStudy();
+ }
pa = dcmdir->GetNextPatient();
- }
-
-}
+ }
+ dcmdir->Delete();
+ return 0;
+
+}
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff