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) {
"subject";
if (verbose)
std::cout << " Subject : [" << subject << "]" << std::endl;
- canOpen =br_subject.LoadFile(subject);
-
+
+ bool subjectFound;
+ canOpen =br_subject.LoadFile(subject);
if (!canOpen)
{
- std::cout << "Hopeless! no 'subject' found" << std::endl;
- throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
- //exit(0); /// \TODO throw an exception !
+ //std::cout << "Hopeless! no 'subject' found" << std::endl;
+ //throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
+
+ std::cout << "Not too much hope! no 'subject' found (Desperate try will be performed -default values- )" << std::endl;
+ subjectFound = false;
}
else
{
- br_subject.FillMap();
+ br_subject.FillMap();
+ subjectFound = true;
}
//br_subject.PrintSelf();
// 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);
+ if (subjectFound)
+ {
+ BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
+ subject_name = b_name.GetStringValue()[0];
+ strPatientName = subject_name;
+ cleanString(subject_name);
+ }
+ else
+ subject_name ="defaultPatName";
+
+ // 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 "));
+ }
+
+ std::string subject_entry;
+ std::string subject_position;
+ std::string subject_date;
+ std::string subject_study_name;
- 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);
+ if (subjectFound)
+ {
+ BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
+ 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");
+ 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");
+ 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");
+ 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);
+ }
+ else // Desperate trick when file 'subject' is missing
+ {
+ subject_entry = "HeadFirst"; // Why not?
+ subject_position = "Supine"; // Why not?
+ strStudyTimeDate = "06_06_06_6_June_1666"; // Why not?
+ subject_date = "6_June_1666"; // Why not?
+ subject_study_name = "defStudyName"; // Why not?
+ }
+ // 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();
br_acqp.LoadFile(strAcqp);
br_acqp.FillMap();
+//std::cout << "out of br_acqp.FillMap " << std::endl;
std::string acqp_scan_name;
std::string acqp_method;
std::string acqp_protocol_location;
BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
acqp_protocol_location = b_protocol_location.GetStringValue()[0];
cleanString(acqp_protocol_location);
-
+
+//std::cout << "out of br_acqp.FillMap 1" << std::endl;
BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
+//std::cout << "out of br_acqp.FillMap 11" << std::endl;
acqp_scan_name = b_scan_name.GetStringValue()[0];
+//std::cout << "out of br_acqp.FillMap 12 [" << acqp_scan_name << "]" << std::endl;
cleanString(acqp_scan_name);
+//std::cout << "out of br_acqp.FillMap 2" << std::endl;
+ BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
+ b_method.PrintSelf();
+ acqp_method = b_method.GetStringValue()[0];
- BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
- acqp_method = b_method.GetStringValue()[0];
cleanString(acqp_method);
-
+//std::cout << "out of br_acqp.FillMap 3" << std::endl;
BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
- //b_list_size.PrintSelf(); //JP
+//std::cout << "out of br_acqp.FillMap 4" << std::endl;
+ //b_list_size.PrintSelf(); //JP
nbSlices = b_list_size.GetIntValue()[0];
-
+//std::cout << "out of br_acqp.FillMap 5" << std::endl;
strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
/* + "." + acqp_protocol_location */ // always the same (in each acquisition)
+ "." + 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() );
} // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
}
-
// =====================================================================
void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
br_method.FillMap();
/* a recuperer :
- ##$PVM_Fov (dimension)
+ ##$PVM_Fov (dimension) // ou plutot RECO_fov !
*/
/*
dans method (pour perfusion seulement?) :
7 1
*/
try {
- DealWithNiveau2(*it,outputDirName );
+ DealWithNiveau2(*it, outputDirName);
}
catch (BrukerHopelessException &e)
{
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];
//std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
// br_reco.PrintSelf();
// std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
-
// -------------------end try reco
std::string mhdDataPixelType;
int pixelSize;
getImhDataType(bDPT, mhdDataPixelType, pixelSize);
-
+
+
+ /*
+
+ // See mail Denis :
+ // En regle generale il vaut mieux que l'on passe par RECO_*
+ // pour extraire les parametres de l'image
+ //
+
BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
double fovX = fov.GetDoubleValue()[0];
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;
+*/
+
+
+// Better we use 'get' accessors from BrukerImage class, as Denis wrote them
+
+ BrukerFieldData fov = br_reco.GetFieldData("RECO_Fov");
+ double fovX = fov.GetDoubleValue()[0];
+ double fovY = fov.GetDoubleValue()[1];
+ if (verbose)
+ std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
+
+ BrukerFieldData spatResol = br_reco.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)
BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
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];
///\ TODO : find a safer way to be sure to read everything!
size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
//return;
throw (e);
}
-
+
serieNumber++;
strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
if (nbInstants==1) // creer un seul fichier .mhd pour toutes les Slices! (images natives)
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" );
{
sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
-
+
/* ----------- Write Dicom Image ---------------*/
MakeDicomImage(buffer_2dseq,
NX,
NY,
nbFrames,
pixelSize,
- fovX/NY, fovY/NY, sliceDistance,
+ //fovX/NY, fovY/NY, sliceDistance,
+ spatResolX, spatResolY, sliceDistance,
output2dseqSliceFileName,
- strPatientName,
+ subject_name,
day,
strStudyUID,
strSerieUID,
);
} // end if dicom
} // end if nbInstants = 1
-
+
else // more than ONE instant
{
// 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,
} // end nbInstants == 1
delete [] buffer_2dseq;
/**/
-
-
+
+
// -----------------------------------------------------
// 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)
{
GDCM_NAME_SPACE::DirListType::iterator it;
char file_name_ident[500];
FILE *fp;
-
+
// Iterate to ALL the objets(files/directories) found in the input directory
for (it = fileNames.begin();
it != fileNames.end();
if (verbose)
std::cout << "--- [" << *it << "] is a file..." << std::endl;
- icode = 0;
- iseparator = 0;
+ icode = 0;
while (code[icode][0] != 0)
- {
+ {
+ iseparator = 0;
while (separator[iseparator][0] != 0)
{
sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g "2dseq_ADC"
if ( loc != std::string::npos )
{
-
+
///\ TODO : find a safer way to be sure to read everything!
unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
fp = fopen ( (*it).c_str(), "rb");
}
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;
-
+
FILE *fp;
fp=fopen(outputMhdFileName, "w");
if (!fp)
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!
- }
- iseparator ++;
- }
- 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;
fileH->Delete();
throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
}
- if (verbose)
- file->Print();
+ //if (verbose)
+ // file->Print();
file->Delete();
fileH->Delete();
git://git.creatis.insa-lyon.fr / creaBruker.git / blobdiff