Program: gdcm
Module: $RCSfile: PhilipsToBrucker.cxx,v $
Language: C++
- Date: $Date: 2005/12/21 15:01:04 $
- Version: $Revision: 1.1 $
+ Date: $Date: 2006/01/26 15:52:42 $
+ 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
#include "gdcmDicomDir.h"
#include "gdcmDicomDirPatient.h"
#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
#include "gdcmDirList.h"
#include "gdcmDebug.h"
#include "gdcmArgMgr.h"
* - explores recursively the given directory
* - keeps the requested series
* - orders the gdcm-readable found Files
- * according their Patient/Study/Serie/Image characteristics
+ * according to their Patient/Study/Serie/Image characteristics
* - fills a single level Directory with *all* the files,
* converted into a Brucker-like Dicom, Intags compliant
- *
+ *
*/
typedef std::map<std::string, gdcm::File*> SortedFiles;
int main(int argc, char *argv[])
{
-/*
START_USAGE(usage)
" \n PhilipsToBrucker :\n ",
- " Explores recursively the given directory, ",
- " ",
- " usage: PhilipsToBrucker dirin=rootDirectoryName ",
- " dirout=outputDirectoryName ",
- " [noshadowseq][noshadow][noseq] [debug] ",
+ " - explores recursively the given directory, ",
+ " - keeps the requested series/ drops the unrequested series ",
+ " - orders the gdcm-readable found Files according to their ",
+ " (0x0010, 0x0010) Patient's Name ",
+ " (0x0020, 0x000e) Series Instance UID ",
+ " (0x0020, 0x0032) Image Position (Patient) ",
+ " (0x0018, 0x1312) In-plane Phase Encoding Direction ",
+ " (0x0018, 0x1060) Trigger Time ",
+ " - fills a single level (*) Directory with *all* the files, ",
+ " converted into a Brucker-like Dicom, InTags compliant ",
+ " (*) actually : creates as many directories as Patients ",
+ " -that shouldn't appear, but being carefull is better ! -",
" ",
- " 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 ",
- " debug : user wants to run the program in 'debug mode' ",
+ " usage: ",
+ " PhilipsToBrucker dirin=rootDirectoryName ",
+ " dirout=outputDirectoryName ",
+ " { [keep= list of seriesNumber to process] ",
+ " | [drop= list of seriesNumber to ignore] } ",
+ " [extent=image suffix (.IMA, .NEMA, .DCM, ...)] ",
+ " [noshadowseq][noshadow][noseq] [verbose] [debug] ",
+ " ",
+ " dirout : will be created if doesn't exist ",
+ " keep : if user wants to process a limited number of series ",
+ " he gives the list of 'SeriesNumber' (tag 0020|0011) ",
+ " drop : if user wants to ignore a limited number of series ",
+ " he gives the list of 'SeriesNumber' (tag 0020|0011) ",
+ " SeriesNumber are short enough to be human readable ",
+ " e.g : 1030,1035,1043 ",
+ " extent : DO NOT forget the leading '.' ! ",
+ " 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
-*/
-const char **usage;
- // ----- Initialize Arguments Manager ------
+ // ----- Initialize Arguments Manager ------
+
gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
if (argc == 1 || am->ArgMgrDefined("usage"))
return 0;
}
- char *dirNamein;
- dirNamein = am->ArgMgrGetString("dirin",(char *)".");
+ const char *dirNamein;
+ dirNamein = am->ArgMgrGetString("dirin",".");
- char *dirNameout;
- dirNameout = am->ArgMgrGetString("dirout",(char *)".");
+ const char *dirNameout;
+ dirNameout = am->ArgMgrGetString("dirout",".");
int loadMode = gdcm::LD_ALL;
if ( am->ArgMgrDefined("noshadowseq") )
if (am->ArgMgrDefined("debug"))
gdcm::Debug::DebugOn();
+
+ bool verbose = am->ArgMgrDefined("verbose");
+
+ int nbSeriesToKeep;
+ int *seriesToKeep = am->ArgMgrGetListOfInt("keep", &nbSeriesToKeep);
+ int nbSeriesToDrop;
+ int *seriesToDrop = am->ArgMgrGetListOfInt("drop", &nbSeriesToDrop);
+ if ( nbSeriesToKeep!=0 && nbSeriesToDrop!=0)
+ {
+ std::cout << "KEEP and DROP are mutually exclusive !" << std::endl;
+ delete am;
+ return 0;
+ }
+
+ const char *extent = am->ArgMgrGetString("extent",".DCM");
+
// if unused Param we give up
if ( am->ArgMgrPrintUnusedLabels() )
{
delete am;
return 0;
}
-
delete am; // we don't need Argument Manager any longer
// ----- Begin Processing -----
+
+ if ( ! gdcm::DirList::IsDirectory(dirNamein) )
+ {
+ std::cout << "KO : [" << dirNamein << "] is not a Directory : " << std::endl;
+ exit(0);
+ }
+ else
+ {
+ std::cout << "OK : [" << dirNamein << "]" << " is a Directory" << std::endl;
+ }
+
+ std::string systemCommand;
+ if ( ! gdcm::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::DirList::IsDirectory(dirNameout) ) // be sure it worked
+ {
+ std::cout << "KO : not a dir : [" << dirNameout << "] (creation failure ?)" << std::endl;
+ exit(0);
+ }
+ else
+ {
+ std::cout << "Directory [" << dirNameout << "]" << " created" << std::endl;
+ }
+ }
+ else
+ {
+ std::cout << "Output Directory [" << dirNameout << "]" << " already exists; Used as is." << std::endl;
+ }
std::string strDirNamein(dirNamein);
- gdcm::DirList dirList(strDirNamein, true);
+ gdcm::DirList dirList(strDirNamein, true); // get recursively the list of files
- /*
- std::cout << "---------------File list found ------------" << std::endl;
+/*
+ std::cout << "---------------List of found files ------------" << std::endl;
dirList.Print();
*/
gdcm::DirListType fileNames;
fileNames = dirList.GetFilenames();
- gdcm::SerieHelper *s;
+ gdcm::SerieHelper *s; // Needed only to may use SerieHelper::AddSeriesDetail()
s = gdcm::SerieHelper::New();
/*
s->AddSeriesDetail(0x0018, 0x1312);
s->Print();
*/
-
-
-
+
gdcm::File *f;
-
-/*
- std::cout << "---------------Print Unique Series identifiers---------" << std::endl;
+ gdcm::FileHelper *fh;
+/*
+ std::cout << "---------------Print Unique Series identifiers---------"
+ << std::endl;
std::string uniqueSeriesIdentifier;
for (gdcm::DirListType::iterator it = fileNames.begin();
uniqueSeriesIdentifier=s->CreateUniqueSeriesIdentifier(f);
std::cout << " [" <<
- uniqueSeriesIdentifier << "]" << std::endl;
-
+ uniqueSeriesIdentifier << "]" << std::endl;
f->Delete();
}
*/
- std::cout << "------------------Print Break levels-----------------" << std::endl;
+ if (verbose)
+ std::cout << "------------------Print Break levels-----------------"
+ << std::endl;
std::string userFileIdentifier;
SortedFiles sf;
-
s->AddSeriesDetail(0x0010, 0x0010, false); // Patient's Name
s->AddSeriesDetail(0x0020, 0x000e, false); // Series Instance UID
s->AddSeriesDetail(0x0020, 0x0032, false); // Image Position (Patient)
it != fileNames.end();
++it)
{
- //std::cout << "File Name : " << *it << std::endl;
f = gdcm::File::New();
- f->SetLoadMode(gdcm::LD_ALL);
+ f->SetLoadMode(loadMode);
f->SetFileName( *it );
f->Load();
+
+ // keep only requested Series
+ std::string strSeriesNumber;
+ int seriesNumber;
+ int j;
+
+ bool keep = false;
+ if (nbSeriesToKeep != 0)
+ {
+ strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
+ seriesNumber = atoi( strSeriesNumber.c_str() );
+ for (j=0;j<nbSeriesToKeep; j++)
+ {
+ if(seriesNumber == seriesToKeep[j])
+ {
+ keep = true;
+ break;
+ }
+ }
+ if ( !keep)
+ {
+ f->Delete();
+ continue;
+ }
+ }
+ // drop all unrequested Series
+ bool drop = false;
+ if (nbSeriesToDrop != 0)
+ {
+ strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
+ seriesNumber = atoi( strSeriesNumber.c_str() );
+ for (j=0;j<nbSeriesToDrop; j++)
+ {
+ if(seriesNumber == seriesToDrop[j])
+ {
+ drop = true;
+ break;
+ }
+ }
+ if (drop)
+ {
+ f->Delete();
+ continue;
+ }
+ }
userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);
//std::cout << " [" <<
// userFileIdentifier << "]" << std::endl;
+
// storing in a map ensures automatic sorting !
sf[userFileIdentifier] = f;
}
std::vector<std::string> tokens;
- std::string fullFilename;
+ std::string fullFilename, lastFilename;
std::string previousPatientName, currentPatientName;
std::string previousSerieInstanceUID, currentSerieInstanceUID;
std::string previousImagePosition, currentImagePosition;
std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection;
- SortedFiles::iterator it2 = sf.begin();
-
- gdcm::Util::Tokenize (it2->first, tokens, "_");
+ std::string writeDir, currentWriteDir;
- previousPatientName = tokens[0];
- previousSerieInstanceUID = tokens[1];
- previousImagePosition = tokens[2];
- previousPhaseEncodingDirection = tokens[3];
- std::cout << "==== new Patient " << currentPatientName << std::endl;
- std::cout << "==== === new Serie " << currentSerieInstanceUID << std::endl;
- std::cout << "==== === === new Position " << currentImagePosition << std::endl;
- std::cout << "==== === === === new PhaseEncodingDirection " << currentImagePosition << std::endl;
- std::cout << "==== === === === " << it2->first << std::endl;
-
- it2++;
+ writeDir = gdcm::Util::NormalizePath(dirNameout);
+ SortedFiles::iterator it2;
+
+ previousPatientName = "";
+ previousSerieInstanceUID = "";
+ previousImagePosition = "";
+ previousPhaseEncodingDirection = "";
- for ( ; it2 != sf.end(); ++it2)
- {
+ int sliceIndex = 0;
+ int frameIndex = 0;
+
+ gdcm::File *currentFile;
+
+ for (it2 = sf.begin() ; it2 != sf.end(); ++it2)
+ {
+ currentFile = it2->second;
+
+ fullFilename = currentFile->GetFileName();
+ lastFilename = gdcm::Util::GetName( fullFilename );
+
+
tokens.clear();
gdcm::Util::Tokenize (it2->first, tokens, "_");
if (previousPatientName != currentPatientName)
{
previousPatientName = currentPatientName;
- std::cout << "==== new Patient " << currentPatientName << std::endl;
+ if (verbose)
+ std::cout << "==== new Patient " << currentPatientName << std::endl;
previousPatientName = currentPatientName;
- previousSerieInstanceUID = currentSerieInstanceUID;
- previousImagePosition = currentImagePosition;
- previousPhaseEncodingDirection = currentPhaseEncodingDirection;
+ previousSerieInstanceUID = ""; //currentSerieInstanceUID;
+ previousImagePosition = ""; //currentImagePosition;
+ previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
+
+ currentWriteDir = writeDir + currentPatientName;
+ if ( ! gdcm::DirList::IsDirectory(currentWriteDir) )
+ {
+ systemCommand = "mkdir " + currentWriteDir;
+ if (verbose)
+ std::cout << systemCommand << std::endl;
+ system ( systemCommand.c_str() );
+ }
}
if (previousSerieInstanceUID != currentSerieInstanceUID)
{
- std::cout << "==== === new Serie " << currentSerieInstanceUID << std::endl;
+ if (verbose)
+ std::cout << "==== === new Serie " << currentSerieInstanceUID
+ << std::endl;
previousSerieInstanceUID = currentSerieInstanceUID;
- previousImagePosition = currentImagePosition;
- previousPhaseEncodingDirection = currentPhaseEncodingDirection;
+ previousImagePosition = ""; //currentImagePosition;
+ previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
}
if (previousImagePosition != currentImagePosition)
{
- std::cout << "==== === === new Position " << currentImagePosition << std::endl;
+ if (verbose)
+ std::cout << "=== === === new Position " << currentImagePosition
+ << std::endl;
previousImagePosition = currentImagePosition;
- previousPhaseEncodingDirection = currentPhaseEncodingDirection;
+ previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
+ sliceIndex += 1;
}
if (previousPhaseEncodingDirection != currentPhaseEncodingDirection)
{
- std::cout << "==== === === === new PhaseEncodingDirection " << currentImagePosition << std::endl;
+ if (verbose)
+ std::cout << "==== === === === new PhaseEncodingDirection "
+ << currentPhaseEncodingDirection << std::endl;
previousPhaseEncodingDirection = currentPhaseEncodingDirection;
- }
- fullFilename = (it2->second)->GetFileName();
- std::cout << "==== === === === " << it2->first << " " << (it2->second)->GetFileName() << " "
- << gdcm::Util::GetName( fullFilename ) <<std::endl;
+ }
+ frameIndex++;
+ if (verbose)
+ std::cout << "--- --- --- --- --- " << (it2->second)->GetFileName()
+ << std::endl;
+ if ( gdcm::Debug::GetDebugFlag())
+ std::cout << "--- --- --- --- --- " << it2->first << " "
+ << (it2->second)->GetFileName() << " "
+ << gdcm::Util::GetName( fullFilename ) << std::endl;
+ // Transform the image to be 'Brucker-Like'
+ // ----------------------------------------
+
+ // Deal with 0x0019, 0x1000 : 'FOV'
+ int nX = currentFile->GetXSize();
+ int nY = currentFile->GetYSize();
+ float pxSzX = currentFile->GetXSpacing();
+ float pxSzY = currentFile->GetYSpacing();
+ char fov[64];
+ sprintf(fov, "%f\\%f",nX*pxSzX, nY*pxSzY);
+ currentFile->InsertEntryString(fov, 0x0019, 0x1000, "DS");
+
+ // Deal with 0x0020, 0x0012 : 'SESSION INDEX'
+ std::string chSessionIndex;
+ if (currentPhaseEncodingDirection == "ROW")
+ chSessionIndex = "1";
+ else
+ chSessionIndex = "2"; // suppose it's "COLUMN" !
+ currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS");
+
+ // Deal with 0x0021, 01020 : 'SLICE INDEX'
+ char chSliceIndex[5];
+ sprintf(chSliceIndex, "%04d", sliceIndex);
+ std::string strChSliceIndex(chSliceIndex);
+ currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, "IS");
+
+ // Deal with 0x0021, 01040 : 'FRAME INDEX'
+ char chFrameIndex[5];
+ sprintf(chFrameIndex, "%04d", frameIndex);
+ currentFile->InsertEntryString(chFrameIndex, 0x0021, 0x1040, "IS");
+
+ std::string strExtent(extent);
+ std::string fullWriteFilename = currentWriteDir + gdcm::GDCM_FILESEPARATOR + lastFilename + strExtent;
+
+ /*
+ systemCommand = "cp " + fullFilename + " " + fullWriteFilename;
+ std::cout << systemCommand << std::endl;
+ system ( systemCommand.c_str() );
+ */
+
+ // Load the pixels in RAM.
+
+ fh = gdcm::FileHelper::New(currentFile);
+ fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
+ fh->SetWriteTypeToDcmExplVR();
+ fh->Write(fullWriteFilename);
+ fh->Delete();
}
}
-
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff