Program: gdcm
Module: $RCSfile: ToInTag.cxx,v $
Language: C++
- Date: $Date: 2006/06/01 10:33:13 $
- Version: $Revision: 1.2 $
+ Date: $Date: 2006/07/17 13:24:59 $
+ Version: $Revision: 1.7 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
* 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 ToInTag :\n ",
+ " \n ToInTag :\n ",
" - explores recursively the given directory, ",
" - keeps the requested series/ drops the unrequested series ",
" - orders the gdcm-readable found Files according to their ",
" 0x0021, 0x1040 : 'FRAME INDEX' ",
" 0x0020, 0x0012 : 'SESSION INDEX' (Acquisition Number) ",
" usage: ",
- " PhilipsToBrucker dirin=rootDirectoryName ",
+ " ToInTag dirin=rootDirectoryName ",
" dirout=outputDirectoryName ",
" { [keep= list of seriesNumber to process] ",
" | [drop= list of seriesNumber to ignore] } ",
" debug : *developer* wants to run the program in 'debug mode' ",
FINISH_USAGE
+ std::cout << "inside ToInTag" << std::endl;
+
// ----- Initialize Arguments Manager ------
gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
{
std::cout << "------------List of found files ------------" << std::endl;
dirList.Print();
+ std::cout << std::endl;
}
gdcm::DirListType fileNames;
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
-
+
+ //uint8_t *imageData; // Useless : pixels will not be loaded
+ // (images are overwritten)
+
for (gdcm::DirListType::iterator it = fileNames.begin();
it != fileNames.end();
++it)
// storing in a map ensures automatic sorting !
sf[userFileIdentifier] = f;
}
+
+ if (verbose)
+ std::cout << " " << std::endl;
std::string fullFilename, lastFilename;
std::string previousPatientName, currentPatientName;
std::string previousImagePosition, currentImagePosition;
std::string previousPhaseEncodingDirection, currentPhaseEncodingDirection;
std::string previousTriggerTime, currentTriggerTime;
+
+ std::string currentStudyUID;
std::string writeDir, currentWriteDir;
std::string currentPatientWriteDir, currentSerieWriteDir,
previousTriggerTime = "";
int sliceIndex = 0; // Is incremented *at the beginning* of processing
- int frameIndex = 1;
+ int frameIndex;
+ if (taggrid)
+ frameIndex = 0;
+ else
+ frameIndex = 1;
+
int flag = 0;
gdcm::File *currentFile;
+
+ std::string defaultStudyUID = gdcm::Util::CreateUniqueUID();
+ std::string defaultSerieUID;
for (it2 = sf.begin() ; it2 != sf.end(); ++it2)
{
fullFilename = currentFile->GetFileName();
lastFilename = gdcm::Util::GetName( fullFilename );
- std::cout << "Rewrite [" <<lastFilename << "]" << std::endl;
+ std::cout << " --------------------------------------------------"
+ << " Rewrite [" <<lastFilename << "]" << std::endl;
tokens.clear();
gdcm::Util::Tokenize (it2->first, tokens, token);
currentImagePosition[0] = 'P';
if (previousPatientName != currentPatientName)
- {
+ {
+ if ( currentFile->GetEntryString(0x0020,0x000d) == gdcm::GDCM_UNFOUND)
+ {
+ if (verbose)
+ std::cout << "--- new Study UID created" << std::endl;
+ defaultStudyUID = gdcm::Util::CreateUniqueUID();
+ currentFile->InsertEntryString(defaultStudyUID, 0x0020, 0x000d, "UI" );
+ }
+
previousPatientName = currentPatientName;
if (verbose)
std::cout << "==== new Patient [" << currentPatientName << "]" << std::endl;
if (verbose)
std::cout << "==== === new Serie [" << currentSerieInstanceUID << "]"
<< std::endl;
+
+ if ( currentFile->GetEntryString(0x0020,0x000e) == gdcm::GDCM_UNFOUND)
+ {
+ if (verbose)
+ std::cout << "--- --- new Serie UID created" << std::endl;
+ defaultSerieUID = gdcm::Util::CreateUniqueUID();
+ currentFile->InsertEntryString(defaultSerieUID, 0x0020, 0x000e, "UI" );
+ }
+
if (split)
{
currentSerieWriteDir = currentPatientWriteDir + gdcm::GDCM_FILESEPARATOR
sliceIndex = 1; // only *one* slice in a given directory
else
sliceIndex += 1;
- }
+ }
+ if (verbose)
+ std::cout << "Slice Index : " << sliceIndex << std::endl;
// We don't split on Row/Column!
/*
chSessionIndex = "1";
}
}
- if (currentFile->IsVRCoherent(0x0020) == 1 )
+ if (currentFile->IsVRCoherent(0x0020) == 1 )
currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, " ");
- else
+ else
currentFile->InsertEntryString(chSessionIndex, 0x0020, 0x0012, "IS");
// Deal with 0x0021, 0x1020 : 'SLICE INDEX'
currentFile->InsertEntryString(strChSliceIndex, 0x0021, 0x1020, stringVR);
currentFile->InsertEntryString(chFrameIndex, 0x0021, 0x1040, stringVR);
+
+
+ std::string strImagePositionPatient = currentFile->GetEntryString(0x0020, 0x0032 );
+ if (strImagePositionPatient == gdcm::GDCM_UNFOUND)
+ {
+ if (verbose)
+ std::cout << "Duplicate ImagePosition into ImagePositionPatient" << std::endl;
+ currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0030), 0x0020, 0x0032, "DS" );
+ }
+ std::string strImageOrientationPatient = f->GetEntryString(0x0020, 0x0037 );
+ if (strImageOrientationPatient == gdcm::GDCM_UNFOUND)
+ {
+ if (verbose)
+ std::cout << "Duplicate ImageOrientation into ImageOrientationPatient" << std::endl;
+ currentFile->InsertEntryString(currentFile->GetEntryString(0x0020, 0x0035), 0x0020, 0x0037, "DS" );
+ }
+
if (taggrid)
frameIndex++;
else
flag = 0;
}
}
+ if (verbose)
+ std::cout << "Frame Index : " << frameIndex << std::endl;
if (split)
// Load the pixels in RAM.
fh = gdcm::FileHelper::New(currentFile);
- fh->GetImageDataRaw(); // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
+ 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)
+
+ // 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;
+
fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE);
if (!fh->Write(fullWriteFilename))
{
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff