bool Bruker2Dicom::Execute()
{
- // ----- Check input values -----
+ // ----- Check input directory name -----
bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl;
}
+ // ----- Check output directory name -----
+
std::string strDirNameOut(OutputDirName);
bool res=CreateDirectory(strDirNameOut);
if (!res) {
// get info for 'Study Description'
- BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
- std::string subject_name = b_name.GetStringValue()[0];
- strPatientName = subject_name;
- cleanString(subject_name);
-
- BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
- std::string subject_entry = b_entry.GetStringValue()[0];
- //cleanString(subject_entry);
- subject_entry = subject_entry.substr(11, subject_entry.size()-11);
+ BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
+ subject_name = b_name.GetStringValue()[0];
+ strPatientName = subject_name;
+ cleanString(subject_name);
+
+ // creation directory : 'nom du patient'
+ std::string tempStringPatDir(OutputDirName);
+ tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name;
+
+ res=CreateDirectory(tempStringPatDir);
+ if (!res) {
+ std::cout << "[" << tempStringPatDir << "] Directory creation failure " << std::endl;
+ throw ( BrukerHopelessException ("Patient directory creation failure "));
+ }
+
+ BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
+ std::string subject_entry = b_entry.GetStringValue()[0];
+ //cleanString(subject_entry);
+ subject_entry = subject_entry.substr(11, subject_entry.size()-11);
- BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
- std::string subject_position = b_position.GetStringValue()[0];
- //cleanString(subject_position);
- subject_position = subject_position.substr(9, subject_position.size()-9);
+ BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
+ std::string subject_position = b_position.GetStringValue()[0];
+ //cleanString(subject_position);
+ subject_position = subject_position.substr(9, subject_position.size()-9);
- BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
- std::string subject_date = b_date.GetStringValue()[0];
- strStudyTimeDate = subject_date;
- cleanString(subject_date);
+ BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
+ std::string subject_date = b_date.GetStringValue()[0];
+ strStudyTimeDate = subject_date;
+ cleanString(subject_date);
- BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
- std::string subject_study_name = b_study_name.GetStringValue()[0];
- subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
- cleanString(subject_date);
-
- // subject_name is already in 'Patient Name'
- strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
+ BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
+ std::string subject_study_name = b_study_name.GetStringValue()[0];
+ subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
+ cleanString(subject_study_name);
+ // subject_name is already in 'Patient Name'
+ strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
+
+ // creation directory : 'nom de la Study'
+
+ std::string tempStringStudyDir(OutputDirName);
+ tempStringStudyDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + strStudyDescr;
+
+ res=CreateDirectory(tempStringStudyDir);
+ if (!res) {
+ std::cout << "[" << tempStringStudyDir << "] Directory creation failure " << std::endl;
+ throw ( BrukerHopelessException ("Study directory creation failure "));
+ }
+
char outputDirName[(unsigned int) PATH_MAX+2];
- strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
- serieNumber = 0;
+ strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+ serieNumber = 0;
instanceNumber = 0;
// -----------------------------------------------------
// Iterate to ALL the objets(files/directories) found in the input directory
// (this is level ZERO)
// each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
// -----------------------------------------------------
-
+
GDCM_NAME_SPACE::DirListType::iterator it;
for (it = fileNames.begin();
+ "." + acqp_scan_name
+ "." + acqp_method.c_str();
- sprintf(outputDirName, "%s%c%s", OutputDirName.c_str(),
+ sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(), //OutputDirName.c_str(),
GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
strSerieDescr.c_str() );
std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
<< " We skip [" << level2Directory << "]" << std::endl;
continue;
- }
+ }
+ catch (BrukerInitException &e)
+ {
+ std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
+ << " We skip [" << level2Directory << "]" << std::endl;
+ continue;
+ }
}
}
}
fileNames = dirList.GetFilenames();
char original2dseqName [(unsigned int) PATH_MAX+2];
+ char original2dseqName_XXX [(unsigned int) PATH_MAX+2];
char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
char outputMhdFileName [(unsigned int) PATH_MAX+2];
if (!canOpen)
{
std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
- throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
+ throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));
//exit(0); /// \TODO throw an exception !
}
//std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
// br_reco.PrintSelf();
// std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
-
// -------------------end try reco
double fovY = fov.GetDoubleValue()[1];
if (verbose)
std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
+
+ BrukerFieldData spatResol = br_method.GetFieldData("PVM_SpatResol");
+ double spatResolX = spatResol.GetDoubleValue()[0];
+ double spatResolY = spatResol.GetDoubleValue()[1];
+ if (verbose)
+ std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl;
+
/// \TODO probabely a more sophisticated accessor will be necessary :
/// (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
fp = fopen(original2dseqName, "rb");
if (!fp)
{
- std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
- throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
- //exit (0);
+ // try 2dseq_Angio2D ?!?
+
+ sprintf( original2dseqName_XXX, "%s%s", original2dseqName, "_Angio2D");
+ fp = fopen(original2dseqName_XXX, "rb");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << original2dseqName << "] nor [" << original2dseqName_XXX << "] for reading" << std::endl;
+ fclose(fp);
+ throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
+ //exit (0);
+ }
}
unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
}
catch (BrukerInitException& e)
{
- std::cout << "an Exception was throw in CreateImageSet ( ); " << e.what()
- << "catched in DealWithNiveau3" << std::endl;
+ if (verbose)
+ std::cout << "an Init Exception was thrown in CreateImageSet ( ); " << e.what()
+ << "catched in DealWithNiveau3" << std::endl;
//return;
throw (e);
}
fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
fprintf(fp, "HeaderSize = %d\n", 0);
- fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
+ //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
+ fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance );
fprintf(fp, "Position = 0 0 %d\n", 0 );
fprintf(fp, "Offset = 0 0 0\n" );
fprintf(fp, "CenterOfRotation = 0 0 0\n" );
NY,
nbFrames,
pixelSize,
- fovX/NY, fovY/NY, sliceDistance,
+ //fovX/NY, fovY/NY, sliceDistance,
+ spatResolX, spatResolY, sliceDistance,
output2dseqSliceFileName,
- strPatientName,
+ subject_name,
day,
strStudyUID,
strSerieUID,
{
// Interleaved !
// it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
-
unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
k = 0;
fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
fprintf(fp, "HeaderSize = %d\n", 0);
- fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // slice distance : no meaning for temporal serie
- fprintf(fp, "Position = 0 0 %d\n", sliceNb );
+ //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); //
+ fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, 1.0 ); //slice distance : no meaning for temporal serie
+ fprintf(fp, "Position = 0 0 %d\n", sliceNb );
fprintf(fp, "Offset = 0 0 0\n" );
fprintf(fp, "CenterOfRotation = 0 0 0\n" );
fprintf(fp, "ElementNumberOfChannels = 1\n" );
NY,
nbInstants,
pixelSize,
- fovX/NY, fovY/NY, sliceDistance,
+ spatResolX, spatResolY, sliceDistance,
+ //fovX/NY, fovY/NY, sliceDistance,
output2dseqSliceFileName,
- strPatientName,
+ subject_name,
day,
strStudyUID,
strSerieUID,
// deal with MatLab-generated Carto file.
// -----------------------------------------------------
- dealWithCarto(fileNames, NX, NY, nbSlices, fovX, fovY, sliceDistance,
+ dealWithCarto(fileNames, NX, NY, nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance,
copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
}
// ===========================================================================================
void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
- double fovX, double fovY, double sliceDistance,
+ /*double fovX, double fovY, */
+ double spatResolX, double spatResolY, double sliceDistance,
char *copyFile, std::string ¤tOutputDirName,
char *outputMhdFileName, char *output2dseqCartoName)
{
// deal with MatLab-generated Carto file.
// -----------------------------------------------------
- char *code[] ={ "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" }; // add more carto file name identifiers if necessary; end with ""
- int icode;
+ char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" }; // add more carto file name identifiers if necessary; end with ""
+ char *separator[] = { "_", ".", "-", "" }; // add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with ""
+ int icode;
+ int iseparator;
GDCM_NAME_SPACE::DirListType::iterator it;
char file_name_ident[500];
FILE *fp;
if (verbose)
std::cout << "--- [" << *it << "] is a file..." << std::endl;
- icode = 0;
-
+ icode = 0;
while (code[icode][0] != 0)
+ {
+ iseparator = 0;
+ while (separator[iseparator][0] != 0)
{
- sprintf(file_name_ident, "2dseq.%s",code[icode]); // e.g "2dseq_ADC"
+ sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g "2dseq_ADC"
+ //if (verbose)
+ // std::cout << "check name ["<<(*it) << "] for string [" << file_name_ident << "]" << std::endl;
std::string::size_type loc = (*it).rfind(file_name_ident);
if ( loc != std::string::npos )
}
fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
+ // ?!? sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
<< NX*NY*sizeof(double)*nbSlices << std::endl;
- std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
+ std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
if (mhd)
{
// Copy the data file in the new directory
currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
system(copyFile);
sprintf(outputMhdFileName, "%s%c%s%s",
- currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
+ currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
if (verbose)
std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
fprintf(fp, "BinaryData = True \n" );
fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
- fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
fprintf(fp, "HeaderSize = %d\n", 0 );
- fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
+ fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, sliceDistance );
fprintf(fp, "Position = 0 0 0\n" );
fprintf(fp, "Offset = 0 0 0\n" );
fprintf(fp, "CenterOfRotation = 0 0 0\n" );
NY,
nbSlices,
8, // pixelSize
- fovX/NY, fovY/NY, sliceDistance,
+ //fovX/NY, fovY/NY, sliceDistance,
+ spatResolX, spatResolY, sliceDistance,
output2dseqCartoName,
- strPatientName,
+ subject_name,
day,
strStudyUID,
strSerieUID,
if (verbose)
std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
break; // don't check for more ident on same file name!
-
- }
- icode++;
- }
- }
- } // end iterate on files
-}
+
+ } // end deal with _ADC, -adc, etc
+ iseparator ++;
+ } // end iterate speparators
+ icode++;
+ } // end iterate code
+ } // end boost::filesystem::is_regular(*it)
+ } // end iterate on all objects (files, dir, etc)
+} // end method
// ==========================================================================================================
else
{
if (verbose)
- std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
+ std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
}
return 1;
br_acqp.SetLoopStructure();
std::vector<int> tempVect = br_acqp.GetLoopStructure() ;
std::map<std::string, BrukerFieldData> map = br_acqp.GetBrukerHeaderMap();
+
bool result = br_acqp.ObjectVaryingProperties.init(map,tempVect);
if (result == false)
{
- throw ( BrukerInitException ("Bruker2Dicom::CreateImageSet failure ") );
+ throw ( BrukerInitException ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
}
br_acqp.SetImageLoopStructure();
imageOrientation = imageSet[i].getRotationMatrixRPS2XYZ();
std::cout << "\t Orientation " ;
for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
- std::cout << imageOrientation[i1][i2] << " ";
+ std::cout << imageOrientation[i1][i2] << " ";CreateImageSet
//std::cout << "\t Abs Time " << imageSet[i].getAbsoluteTimePosition();
std::cout << "\t Relat Time " << imageSet[i].getRelativeTimePosition();
fileH->Delete();
throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
}
- if (verbose)
- file->Print();
+ //if (verbose)
+ // file->Print();
file->Delete();
fileH->Delete();