Program: gdcm
Module: $RCSfile: ToInTag.cxx,v $
Language: C++
- Date: $Date: 2007/05/23 14:18:04 $
- Version: $Revision: 1.11 $
+ Date: $Date: 2009/01/19 17:05:13 $
+ Version: $Revision: 1.21 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmFileHelper.h"
#include "gdcmDirList.h"
#include "gdcmDebug.h"
-#include "gdcmArgMgr.h"
#include "gdcmUtil.h"
#include "gdcmSerieHelper.h"
+#include "gdcmArgMgr.h"
+
#include <iostream>
/**
" - 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 ! -",
+ " -that shouldn't appear, but being carefull is better!- ",
" or ",
" - fills a tree-like structure of directories as : ",
" - Patient ",
" -- Serie ",
" --- Position ",
- " Images are (sorted by Trigger Time / ",
- " Encoding Direction (Row, Column) ",
- " use : ",
+ " ---- Images (sorted by Trigger Time / ",
+ " Encoding Direction (Row, Column) ",
+ " ",
+ " Note : when (0008|1090) [Model Name ] equals 'TrioTim ' : ",
+ " - (0008|103e)[Series Description ] is checked for ",
+ " '90' (-> COL) or '0' (-> ROW) ",
+ " - (0x0020, 0x000e) [Series Instance UID] is NOT dealt with, ",
+ " since row an col tagging are in 2 different Series ",
+ " DO NOT supply a directory holding different exams ",
+ " for the same Slice level! ",
+ " uses : ",
" 0x0021, 0x1020 : 'SLICE INDEX' ",
" 0x0021, 0x1040 : 'FRAME INDEX' ",
" 0x0020, 0x0012 : 'SESSION INDEX' (Acquisition Number) ",
+ " ",
" usage: ",
+ " ----- ",
" ToInTag dirin=rootDirectoryName ",
" dirout=outputDirectoryName ",
" { [keep= list of seriesNumber to process] ",
" | [drop= list of seriesNumber to ignore] } ",
" [taggrid] [skel] ",
- " [input = {ACR|DCM}] ",
+ " [input = {ACR|DCM|IDO}] ",
" [extent=image suffix (.IMA, .NEMA, .DCM, ...)] ",
- " [listonly] [split] ",
+ " [listonly] [split] [rubout] ",
" [noshadowseq][noshadow][noseq] [verbose] [debug] ",
" ",
" dirout : will be created if doesn't exist ",
" he gives the list of 'SeriesNumber' (tag 0020|0011) ",
" SeriesNumber are short enough to be human readable ",
" e.g : 1030,1035,1043 ",
- " taggrid : user knows all the images are 'grid' -ie : not 'col', not 'raw'",
+ " taggrid : user knows all the images are 'grid' -ie: not 'col', not 'raw'-",
" extent : DO NOT forget the leading '.' ! ",
+ " input : IDO when *realy* old libIDO images ",
" skel: name skeleton eg : patName_1.nema -> skel=patName_ ",
" split: creates a tree-like structure of directories as : ",
" - Patient ",
" -- Serie ",
" --- Position ",
- " Images are (sorted by Trigger Time / ",
- " Encoding Direction (Row, Column) ",
+ " ---- Images (sorted by Trigger Time / ",
+ " Encoding Direction (Row, Column) ",
+ " rubout : user asks to rubout burnt-in image number ",
" 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 : *developer* wants to run the program in 'debug mode' ",
FINISH_USAGE
+
+ enum Index
+ {
+ IND_PatientName,
+ IND_SerieInstanceUID,
+ IND_ImagePosition,
+ IND_TriggerTime,
+ IND_PhaseEncodingDirection,
+ IND_seriesDescription,
+ IND_FileName
+ };
+
std::cout << "inside ToInTag" << std::endl;
// ----- Initialize Arguments Manager ------
}
const char *dirNamein;
- dirNamein = am->ArgMgrGetString("dirin",".");
+ dirNamein = am->ArgMgrGetString("dirin",".");
const char *dirNameout;
- dirNameout = am->ArgMgrGetString("dirout",".");
+ dirNameout = am->ArgMgrGetString("dirout",".");
int loadMode = GDCM_NAME_SPACE::LD_ALL;
if ( am->ArgMgrDefined("noshadowseq") )
int verbose = am->ArgMgrDefined("verbose");
int split = am->ArgMgrDefined("split");
int listonly = am->ArgMgrDefined("listonly");
-
+
+ bool rubout = ( 0 != am->ArgMgrDefined("rubout") );
+
int nbSeriesToKeep;
int *seriesToKeep = am->ArgMgrGetListOfInt("keep", &nbSeriesToKeep);
int nbSeriesToDrop;
return 0;
}
- int taggrid = am->ArgMgrDefined("taggrid");
-
- int hasSkel = am->ArgMgrDefined("skel");
+ bool taggrid = ( 0 != am->ArgMgrDefined("taggrid") );
+
+ bool hasSkel = ( 0 != am->ArgMgrDefined("hasSkel") );
const char *skel;
if (hasSkel)
- skel = am->ArgMgrGetString("skel");
+ skel = am->ArgMgrGetString("skel");
const char *extent = am->ArgMgrGetString("extent",".DCM");
+ const char *input = am->ArgMgrGetString("input","DCM");
// if unused Param we give up
if ( am->ArgMgrPrintUnusedLabels() )
{
std::cout << "Output Directory [" << dirNameout << "] already exists; Used as is." << std::endl;
}
+
+
std::string strDirNamein(dirNamein);
GDCM_NAME_SPACE::DirList dirList(strDirNamein, true); // get recursively the list of files
GDCM_NAME_SPACE::DirListType fileNames;
fileNames = dirList.GetFilenames();
- GDCM_NAME_SPACE::SerieHelper *s; // Needed only to may use SerieHelper::AddSeriesDetail()
+ GDCM_NAME_SPACE::SerieHelper *s; // Needed to use SerieHelper::AddSeriesDetail()
s = GDCM_NAME_SPACE::SerieHelper::New();
std::string token = "%%%"; // Hope it's enough!
std::vector<std::string> tokens;
std::vector<std::string> tokensForFileName;
- // For Siemens pb, we need Station Name
-
+ // For Siemens pb, we need Manufacturer's Model Name
+ // (We read only the first file, to know)
GDCM_NAME_SPACE::DirListType::iterator it1 = fileNames.begin();
f = GDCM_NAME_SPACE::File::New();
f->SetLoadMode(GDCM_NAME_SPACE::LD_ALL);
f->SetFileName( *it1 );
f->Load();
- std::string stationName = f->GetEntryString(0x0008,0x1010);
+ std::string modelName = f->GetEntryString(0x0008,0x1090);
f->Delete();
/*
if (verbose)
std::cout << "------------------Print Break levels-----------------" << std::endl;
- std::string userFileIdentifier;
+ std::string userFileIdentifier;
SortedFiles sf;
s->AddSeriesDetail(0x0010, 0x0010, false); // Patient's Name
- if ( stationName != "MRC35150" ) // for Siemens MRC35150, don't deal with 'Series Instance UID'
+ // for Siemens TrioTim, don't deal with 'Series Instance UID'
+ if ( !GDCM_NAME_SPACE::Util::DicomStringEqual(modelName,"TrioTim") )
s->AddSeriesDetail(0x0020, 0x000e, false); // Series Instance UID
else
s->AddSeriesDetail(0x9999, 0x9999, false); // dirty trick to ignore 'Series Instance UID'
- s->AddSeriesDetail(0x0020, 0x0032, false); // Image Position (Patient)
- s->AddSeriesDetail(0x0018, 0x1060, true); // Trigger Time (true: convert to keep numerical order)
- s->AddSeriesDetail(0x0018, 0x1312, false); // In-plane Phase Encoding Direction
- s->AddSeriesDetail(0x0008, 0x103e, false); // Series Description (special Siemens ...)
+ s->AddSeriesDetail(0x0020, 0x0032, false); // Image Position (Patient)
+ s->AddSeriesDetail(0x0018, 0x1060, true); // Trigger Time (true: convert to keep numerical order)
+ s->AddSeriesDetail(0x0018, 0x1312, false); // In-plane Phase Encoding Direction
+ s->AddSeriesDetail(0x0008, 0x103e, false); // Series Description (special Siemens ...)
//uint8_t *imageData; // Useless : pixels will not be loaded
// (images are overwritten)
// keep only requested Series
bool keep = false;
if (nbSeriesToKeep != 0)
- {
+ {
strSeriesNumber = f->GetEntryString(0x0020, 0x0011 );
seriesNumber = atoi( strSeriesNumber.c_str() );
for (j=0;j<nbSeriesToKeep; j++)
f->Delete();
continue;
}
- }
+ }
- userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);
+ userFileIdentifier=s->CreateUserDefinedFileIdentifier(f);
tokens.clear();
- GDCM_NAME_SPACE::Util::Tokenize (userFileIdentifier, tokens, token);
-
+ GDCM_NAME_SPACE::Util::Tokenize (userFileIdentifier, tokens, token);
+
int imageNum; // Within FileName
char newName[1024];
-
- if ( tokens[3] == "gdcmUnfound") // sometimes Trigger Time is not found. CreateUserDefinedFileIdentifier is not aware of the pb.
+
+ // sometimes Trigger Time is not found.
+ // CreateUserDefinedFileIdentifier is not aware of the pb.
+ // We use File name instead (hope it's significant)
+
+ if ( tokens[IND_TriggerTime] == GDCM_NAME_SPACE::GDCM_UNFOUND)
{
///this is a trick to build up a lexicographical compliant name :
/// eg : fich001.ima vs fich100.ima as opposed to fich1.ima vs fich100.ima
imageNum = atoi ( tokensForFileName[0].c_str() );
// probabely we could write something much more complicated using C++ !
sprintf (newName, "%s%06d%s", skel, imageNum, extent);
- tokens[3] = newName;
+ tokens[IND_TriggerTime] = newName;
tokensForFileName.clear();
}
else
- tokens[3] = name;
-
+ tokens[IND_TriggerTime] = name;
+
+ // Patient's Name
+ // Series Instance UID
+ // Image Position (Patient)
+ // Trigger Time
+ // In-plane Phase Encoding Direction
+ // Series Description
+ // FileName
- userFileIdentifier = tokens[0] + token + tokens[1] + token + tokens[2] + token
- + tokens[3] + token + tokens[4] + token + tokens[5] + token;
- }
+ userFileIdentifier = tokens[IND_PatientName] + token + tokens[IND_SerieInstanceUID] + token + tokens[IND_ImagePosition] + token
+ + tokens[IND_TriggerTime] + token + tokens[IND_PhaseEncodingDirection] + token + tokens[IND_seriesDescription] + token
+ + tokens[IND_FileName] + token;
+ }
+
if (verbose)
std::cout << "[" << userFileIdentifier << "] : " << *it << std::endl;
frameIndex = 0;
else
frameIndex = 1;
-
+
int flag = 0;
GDCM_NAME_SPACE::File *currentFile;
std::string defaultStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
std::string defaultSerieUID;
-
+
for (it2 = sf.begin() ; it2 != sf.end(); ++it2)
{
currentFile = it2->second;
fullFilename = currentFile->GetFileName();
- lastFilename = GDCM_NAME_SPACE::Util::GetName( fullFilename );
- std::cout << " --------------------------------------------------"
- << " Rewrite [" <<lastFilename << "]" << std::endl;
+ lastFilename = GDCM_NAME_SPACE::Util::GetName( fullFilename );
+ if (verbose)
+ std::cout <<" ------------------------------------------------------------------------------"
+ << std::endl << " Deal with [" << it2->first << "] : ["<<fullFilename << "]"
+ << std::endl;
tokens.clear();
GDCM_NAME_SPACE::Util::Tokenize (it2->first, tokens, token);
-
- currentPatientName = tokens[0];
- currentSerieInstanceUID = tokens[1];
- currentImagePosition = tokens[2];
- currentTriggerTime = tokens[3];
- currentPhaseEncodingDirection = tokens[4];
- seriesDescription = tokens[5]; // For Siemens pb
+
+ currentPatientName = tokens[IND_PatientName];
+ currentSerieInstanceUID = tokens[IND_SerieInstanceUID];
+ currentImagePosition = tokens[IND_ImagePosition];
+ currentTriggerTime = tokens[IND_TriggerTime];
+ currentPhaseEncodingDirection = tokens[IND_PhaseEncodingDirection];
+ seriesDescription = tokens[IND_seriesDescription]; // For Siemens pb
if ( currentImagePosition[0] == '-')
currentImagePosition[0] = 'M';
currentFile->InsertEntryString("0.\\0.\\0.",0x0020, 0x0032, "DS" );
}
- // Add a default ImagePositionPatient to avoid confusion at post processing time
+ // Add a default ImageOrientationPatient to avoid confusion at post processing time
if ( currentFile->GetEntryString(0x0020,0x0037) == GDCM_NAME_SPACE::GDCM_UNFOUND &&
currentFile->GetEntryString(0x0020,0x0035) == GDCM_NAME_SPACE::GDCM_UNFOUND )
{
currentFile->InsertEntryString("1.\\0.\\0.\\0.\\1.\\0.",0x0020, 0x0037, "DS" );
}
-
+
if (previousPatientName != currentPatientName)
{
- if ( currentFile->GetEntryString(0x0020,0x000d) == GDCM_NAME_SPACE::GDCM_UNFOUND)
+ if ( currentFile->GetEntryString(0x0020,0x000d) == GDCM_NAME_SPACE::GDCM_UNFOUND) // Study UID
{
if (verbose)
std::cout << "--- new Study UID created" << std::endl;
defaultStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
- currentFile->InsertEntryString(defaultStudyUID, 0x0020, 0x000d, "UI" );
}
previousPatientName = currentPatientName;
system ( systemCommand.c_str() );
}
}
+ currentFile->InsertEntryString(defaultStudyUID, 0x0020, 0x000d, "UI" );
+
- if ( stationName != "MRC35150" ) // for Siemens MRC35150, don't deal with 'Series Instance UID'
+ if ( GDCM_NAME_SPACE::Util::DicomStringEqual(modelName,"TrioTim") ) // for Siemens TrioTim , don't deal with 'Series Instance UID'
if (previousSerieInstanceUID != currentSerieInstanceUID)
{
- if (verbose)
+ if (verbose)
std::cout << "==== === new Serie [" << currentSerieInstanceUID << "]"
<< std::endl;
if (verbose)
std::cout << "--- --- new Serie UID created" << std::endl;
defaultSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
- currentFile->InsertEntryString(defaultSerieUID, 0x0020, 0x000e, "UI" );
- }
-
+ // currentFile->InsertEntryString(defaultSerieUID, 0x0020, 0x000e, "UI" );
+ }
+
if (split)
{
currentSerieWriteDir = currentPatientWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
previousImagePosition = ""; //currentImagePosition;
previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
}
- // end of stationName != "MRC35150"
-
+ currentFile->InsertEntryString(defaultSerieUID, 0x0020, 0x000e, "UI" );
+
+ // end of modelName != "TrioTim "
+
if (previousImagePosition != currentImagePosition)
{
frameIndex = 1;
else
sliceIndex += 1;
}
- if (verbose)
- std::cout << "Slice Index : " << sliceIndex << std::endl;
// We don't split on Row/Column!
/*
if (previousPhaseEncodingDirection != currentPhaseEncodingDirection)
{
- if (verbose)
+ if (verbose)
std::cout << "==== === === === new PhaseEncodingDirection ["
<< currentPhaseEncodingDirection << "]" << std::endl;
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR
+ currentPhaseEncodingDirection;
systemCommand = "mkdir " + currentPhaseEncodingDirectionWriteDir;
- system (systemCommand.c_str());
- }
-
+ system (systemCommand.c_str());
+ }
+
previousPhaseEncodingDirection = currentPhaseEncodingDirection;
- }
-*/
-
- if (verbose)
- std::cout << "--- --- --- --- --- " << (it2->second)->GetFileName()
- << std::endl;
+ }
+*/
if ( GDCM_NAME_SPACE::Debug::GetDebugFlag())
std::cout << "--- --- --- --- --- " << it2->first << " "
std::string chSessionIndex;
// CLEANME
-
if (taggrid)
{
chSessionIndex = "1";
else
{
/* for SIEMENS MRI :
- D 0008|1010 [SH] [Station Name ] [MRC35150]
+ D 0008|1090 [LO] [Manufacturer's Model Name ] [Triotim ]
we have to deal with :
- D 0008|103e [LO] [Series Description ] [fl2d9_line PA 15 90deg]
+ D 0008|103e [LO] [Series Description ] [fl2d9_line PA 15 90deg] or anything that contains '90' !
D 0008|103e [LO] [Series Description ] [fl2d9_line PA 15 0deg ]
(everything is flagged as 'ROW')
- */
- if ( stationName == "MRC35150" )
+ */
+
+ if ( GDCM_NAME_SPACE::Util::DicomStringEqual(modelName,"TrioTim") )
{
- if ( memcmp(seriesDescription.c_str(), "fl2d9linePA1590deg", 18) )
- chSessionIndex = "1";
- else if ( memcmp(seriesDescription.c_str(), "fl2d9linePA150deg", 18) )
- chSessionIndex = "2";
+ if (seriesDescription.find("90", 0) != std::string::npos)
+ chSessionIndex = "1"; // 90 deg -> COL
+ else if (seriesDescription.find("0", 0)!= std::string::npos)
+ chSessionIndex = "2"; // 0 deg -> ROW
else
{
- std::cout << "====================== seriesDescription "
- << " neither fl2d9_line PA 15 90deg nor fl2d9_line PA 15 0deg (?!?) : ["
+ std::cout << "====================== seriesDescription doesn't contain"
+ << " neither '90' nor '0' (?!?) : ["
<< seriesDescription << "]" << std::endl;
chSessionIndex = "1";
}
}
}
}
+
if (currentFile->IsVRCoherent(0x0020) == 1 )
currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, " ");
else
stringVR = "IS";
currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, stringVR);
- currentFile->InsertEntryString(chFrameIndex, 0x0021, 0x1040, stringVR);
-
-
+ currentFile->InsertEntryString(chFrameIndex, 0x0021, 0x1040, stringVR);
+
+ if (verbose) {
+ std::cout << "0x0021, 0x1020 : strChSliceIndex " << strChSliceIndex << std::endl;
+ std::cout << "0x0021, 0x1040 : chFrameIndex " << chFrameIndex << std::endl;
+ std::cout << "0x0020, 0x0012 : chSessionIndex " << chSessionIndex << std::endl;
+ }
+
std::string strImagePositionPatient = currentFile->GetEntryString(0x0020, 0x0032 );
if (strImagePositionPatient == GDCM_NAME_SPACE::GDCM_UNFOUND)
{
if (strImageOrientationPatient == GDCM_NAME_SPACE::GDCM_UNFOUND)
{
if (verbose)
- std::cout << "Duplicate ImageOrientation into ImageOrientationPatient" << std::endl;
+ std::cout << "Duplicate ImageOrientation into ImageOrientationPatient" << std::endl;
currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0035), 0x0020, 0x0037, "DS" );
}
-
- if (taggrid)
+
+ if (taggrid || strcmp(input, "IDO")==0 || strcmp(input, "ido")==0 )
frameIndex++;
else
{
flag = 0;
}
}
- if (verbose)
- std::cout << "Frame Index : " << frameIndex << std::endl;
if (split)
else
fullWriteFilename = currentPatientWriteDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
+ lastFilename + strExtent;
-
- /*
- systemCommand = "cp " + fullFilename + " " + fullWriteFilename;
- std::cout << systemCommand << std::endl;
- system ( systemCommand.c_str() );
- */
// Load the pixels in RAM.
fh = GDCM_NAME_SPACE::FileHelper::New(currentFile);
uint8_t *imageData = fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
- fh->SetWriteTypeToDcmExplVR();
- // We didn't modify pixels -> keep unchanged the following :
+ fh->SetWriteTypeToDcmExplVR();
+
+ if (rubout) {
+ // Put to Black the burnt-in number.
+ nX = currentFile->GetXSize();
+ nY = currentFile->GetYSize();
+ for(int y=nY-15; y<nY; y++)
+ for(int x=nX/3; x<nX/2+50; x++)
+ imageData[ y*nX*2 + x ] = 0;
+ }
+
+ // We didn't make any computation on the pixels -> keep unchanged the following :
// 'Media Storage SOP Class UID' (0x0002,0x0002)
// 'SOP Class UID' (0x0008,0x0016)
// 'Image Type' (0x0008,0x0008)
- // 'Conversion Type' (0x0008,0x0064)
-
- // Put to Black the burnt-in number.
- nX = currentFile->GetXSize();
- nY = currentFile->GetYSize();
- for(int y=nY-15; y<nY; y++)
- for(int x=nX/3; x<nX/2+50; x++)
- imageData[ y*nX*2 + x ] = 0;
-
+ // 'Conversion Type' (0x0008,0x0064)
fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
+
if (!fh->Write(fullWriteFilename))
{
std::cout << "Fail to write :[" << fullWriteFilename << "]"
}
return 0;
}
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff