Program: gdcm
Module: $RCSfile: ToInTag.cxx,v $
Language: C++
- Date: $Date: 2007/05/23 14:18:04 $
- Version: $Revision: 1.11 $
+ Date: $Date: 2007/05/29 10:36:10 $
+ Version: $Revision: 1.12 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
" - 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] ",
" 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 '.' ! ",
" 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) ",
" 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 ",
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
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();
/*
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'
frameIndex = 0;
else
frameIndex = 1;
-
+
int flag = 0;
GDCM_NAME_SPACE::File *currentFile;
fullFilename = currentFile->GetFileName();
lastFilename = GDCM_NAME_SPACE::Util::GetName( fullFilename );
- std::cout << " --------------------------------------------------"
- << " Rewrite [" <<lastFilename << "]" << std::endl;
+ std::cout <<" ------------------------------------------------------------------------------"
+ << std::endl << " Deal with [" << it2->first << "] : ["<<fullFilename << "]"
+ << std::endl;
tokens.clear();
GDCM_NAME_SPACE::Util::Tokenize (it2->first, tokens, token);
}
}
- 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)
{
previousImagePosition = ""; //currentImagePosition;
previousPhaseEncodingDirection = ""; //currentPhaseEncodingDirection;
}
- // end of stationName != "MRC35150"
-
+ // 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!
/*
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) != -1)
+ chSessionIndex = "1"; // 90 deg -> COL
+ else if (seriesDescription.find("0", 0)!= -1)
+ 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" );
}
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 :
- // 'Media Storage SOP Class UID' (0x0002,0x0002)
- // 'SOP Class UID' (0x0008,0x0016)
- // 'Image Type' (0x0008,0x0008)
- // 'Conversion Type' (0x0008,0x0064)
+ fh->SetWriteTypeToDcmExplVR();
// 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;
-
+ 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)
fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
+
if (!fh->Write(fullWriteFilename))
{
std::cout << "Fail to write :[" << fullWriteFilename << "]"
}
return 0;
}
+
projects / gdcm.git / commitdiff